Why Isn’t My Baby’s Reflux Medication Working?

By Dr. Jennifer Harris

Your baby has finally been prescribed medication for reflux.

You hoped this would be the turning point.

But days—or perhaps weeks—later, your baby is still crying, arching, refusing feeds or waking uncomfortable.

Maybe the medication seemed to help initially but gradually stopped working.

Or perhaps you're seeing absolutely no difference at all.

Parents often reach this point feeling incredibly discouraged.

“If reflux is the problem, why isn't the reflux medication working?”

There isn't one answer.

Sometimes the medication or dose needs reviewing. Sometimes the way a medication is being given affects how well it works. Sometimes another treatment may be more appropriate.

But there is another important possibility:

Not every symptom being attributed to reflux is necessarily being caused by acid reflux.

When treatment isn't producing the expected improvement, the goal shouldn't automatically be to give a baby more medication.

It's an opportunity to step back and ask:

Are we treating the right problem, with the right treatment, in the right way?

What medications are used for reflux in babies?

When medication is clinically indicated for gastroesophageal reflux disease (GERD), clinicians may use medicines that reduce stomach acid.

Two categories parents commonly encounter are:

H2-receptor antagonists (H2 blockers), such as famotidine.

and

Proton pump inhibitors (PPIs), such as omeprazole, esomeprazole or lansoprazole.

These medications work differently, but both are intended to reduce gastric acidity.

That distinction is important because reflux medication doesn't necessarily prevent stomach contents from travelling upward. Instead, acid-suppressing medication aims to reduce acidity when refluxed stomach contents are causing acid-related injury or symptoms.

So if your baby continues to visibly spit up while taking acid-suppressing medication, that alone doesn't necessarily mean the medication has “failed.” The question is whether the problem the medication was intended to treat is improving.

Does every baby with reflux need medication?

No.

Reflux is extremely common during infancy and many healthy babies regularly bring milk back up because their digestive system is still developing. If a baby is comfortable, feeding well and growing appropriately, medication usually isn't needed simply because they spit up.

Medication may be considered in selected babies when a clinician believes reflux is causing troublesome symptoms or complications consistent with GERD. This is why the distinction between GER and GERD matters.

The goal isn't to medicate normal infant reflux.

The goal is to identify babies who genuinely need treatment and use that treatment appropriately.

Why might reflux medication seem not to work?

There are several possibilities.

A clinician reviewing a baby who continues to struggle may want to consider:

• Whether reflux is actually responsible for the symptoms

• Whether the medication is appropriate for the problem being treated

• Whether the dose remains appropriate

• Whether the baby has grown significantly since the medication was prescribed

• How and when the medication is being administered

• Whether enough time has been allowed to assess the response

• Whether another medication or treatment approach would be more appropriate

• Whether another medical or feeding problem is contributing

• Whether the original pain has improved but feeding behaviour has changed

  
  

The important point is that persistent symptoms deserve reassessment rather than automatic medication escalation.

Could my baby have outgrown their dose?

Possibly.

Babies grow incredibly quickly and medication prescribed according to a baby's weight may need periodic review as that baby grows. Because of this, a treatment plan that was appropriate when a baby weighed considerably less may not necessarily remain appropriate indefinitely.

That doesn't mean parents should increase a medication dose themselves. What it does mean is that if a medication previously seemed helpful but symptoms have returned—or if symptoms were never adequately controlled—it may be reasonable to ask the prescribing clinician to review the baby's current weight, dose and overall treatment plan.

Medication dosing in infants should always be individualized and reviewed by an appropriately qualified prescriber.

Does the timing of reflux medication matter?

For some medications, yes.

Certain proton pump inhibitors work most effectively when administered in relation to feeding because of how they act on acid-producing cells in the stomach. The formulation also matters because infant medications, including those most commonly prescribed for reflux, may be supplied as compounded liquids, suspensions, granules or other preparations, and instructions can vary depending on the specific product.

This is why I don't recommend applying generic online instructions to every baby's medication. Instead, ask the prescriber or pharmacist:

Exactly how should this particular medication and formulation be given?

Should it be given in relation to a feed?

How should it be measured, mixed or stored?

Are there foods, milk or other medicines that affect how it should be administered?

Correct administration can be an important part of evaluating whether a treatment is actually effective.

How quickly should reflux medication work?

This depends on the medication and what is being treated.

Parents sometimes expect the first dose of a PPI to immediately transform their baby's symptoms but that just isn't always realistic. Acid suppression develops over time, and irritated tissue may also need time to heal.

On the other hand, if a baby has been appropriately treated for a reasonable period and there is no meaningful improvement—or symptoms are worsening—the answer shouldn't necessarily be to keep waiting indefinitely. Instead, the treatment plan and diagnosis may need reviewing. Your baby's prescriber can tell you what response timeline is reasonable for the specific medication and clinical situation.

My baby still spits up on medication. Does that mean it isn't working?

Not necessarily.

This is one of the most important things to understand about acid-suppressing medication: PPIs and H2 blockers reduce acid but they do not necessarily stop the physical act of reflux. A baby may therefore continue to regurgitate or spit up while taking medication.

Therefore, if the purpose of treatment is to reduce acid-related pain or allow esophageal irritation to heal, the outcome we're looking for isn't necessarily:

“My baby never spits up anymore.”

Instead, we may be looking at:

Is feeding more comfortable?

Is there less distress?

Is the baby able to maintain intake?

Are clinically significant acid-related symptoms improving?

This is another reason treatment needs to be individualized.

What if the medication initially worked and then stopped?

There are several possible explanations.

One is that the baby has grown and the treatment plan needs reassessment. Another is that symptoms have changed or another problem has emerged.

With some medications, particularly H2 blockers, clinicians also consider the possibility of tachyphylaxis—a reduction in effectiveness that can occur with repeated use over time. This doesn't mean every baby whose famotidine appears less effective has developed tolerance but a return of symptoms does mean the treatment deserves review rather than assuming the solution is simply to keep doing the same thing indefinitely.

What if the medication seems to make my baby worse?

Parents sometimes report increased gastrointestinal symptoms, changes in stool, abdominal discomfort or other changes after beginning or adjusting medication.

Medications can have side effects, and individual babies can respond differently.

If you notice a clear change after starting a medicine or changing the dose, tell the prescribing clinician, and try to give them specific information. Think about the following questions:

What changed?

When did it begin?

How soon after the medication is given does it happen?

Was anything else changed at the same time?

What happens on different days?

That timeline can be much more useful than simply saying the medication “doesn't agree with” the baby.

Don't stop a prescribed reflux medication solely on the basis of general information online. Discuss suspected side effects and the safest next steps with the prescriber.

Could another reflux medication work better?

Sometimes a clinician may decide that a different medication or treatment strategy is more appropriate.

Different reflux medications work in different ways, and individual circumstances matter.

But the decision shouldn't simply be: Medication A didn't work, so let's keep trying stronger medication until something does.

Instead, before changing treatment, I want to understand why the current plan isn't working. I like to ask:

Is the diagnosis correct?

Is the dose appropriate?

Is administration appropriate?

Was the medication given an adequate trial?

Are the symptoms we're monitoring actually acid-related?

Is there another condition contributing?

That reassessment helps us use medication thoughtfully and effectively rather than reflexively.

Could this actually be cow's milk protein allergy?

Sometimes symptoms attributed to reflux overlap with symptoms associated with cow's milk protein allergy (CMPA).

Depending on the individual baby, a clinician may consider the broader history, including:

• Gastrointestinal symptoms

• Stool changes

• Skin symptoms

• Feeding difficulties

• Growth

• The timing of symptoms

• Response to previous dietary or formula changes

  
  

Reflux alone doesn't diagnose CMPA; likewise, mucus, eczema, crying or gas individually don't prove that a baby has an allergy. But, if a baby isn't responding as expected to reflux treatment, it can be appropriate to reconsider whether another gastrointestinal problem is contributing.

Could it be a feeding or swallowing problem?

Yes.

Some feeding and swallowing difficulties can look remarkably similar to reflux.

A baby might:

• Cough during feeds

• Choke

• Gag

• Pull away

• Become congested

• Sound wet or gurgly

• Struggle to coordinate sucking, swallowing and breathing

• Take very small volumes

• Become increasingly distressed during feeds

  
  

These symptoms shouldn't automatically be treated as acid reflux. If your baby repeatedly coughs, chokes, experiences breathing difficulty or has other concerning symptoms during feeding, tell their healthcare provider. Depending on the clinical picture, a feeding or swallowing evaluation may be appropriate.

Could the reflux be better but feeding still be difficult?

Absolutely.

This is one of the most important concepts for families dealing with prolonged reflux and feeding difficulties.

Imagine a baby repeatedly experiences:

Hunger → feeding → pain.

They learn that feeding predicts discomfort and at first, they stop only when something hurts. Then, after enough repetitions, they may begin anticipating the discomfort. Eventually, they may:

• Pull away earlier in feeds

• Cry when placed into the feeding position

• Turn away when they see the bottle

• Close their mouth

• Feed only while distracted

• Feed primarily while drowsy or asleep

• 
  

Now imagine that the original reflux pain is successfully treated. The pain may be gone but baby doesn't necessarily know that because they've already learned: Feeding isn't safe or comfortable. At that point, increasing reflux medication may not resolve the remaining feeding problem and the underlying medical trigger and the baby's learned feeding response may need to be considered separately.

Why does my baby only feed while asleep despite taking reflux medication?

This is a pattern I would take seriously.

Parents sometimes say:

“The medication must not be working because my baby still refuses every bottle awake—but drinks perfectly asleep.”

Possibly.

But we also need to consider whether feeding aversion has developed. Sleep feeding can allow some babies to eat with less behavioural resistance and parents come to quite understandably rely on it because their baby needs nutrition.

However, if your baby consistently needs to be drowsy or asleep to eat, the question becomes: Why is awake feeding difficult?

Simply increasing acid suppression may not answer that question.

Could feeding pressure be keeping the problem going?

Sometimes.

And this is not about blaming parents. When a baby doesn't eat, parents become frightened. They may have been told to achieve a specific daily intake or may already be worried about growth. Some families are asked to come in for weekly (or sometimes even more frequent) weight checks. It is a lot of pressure on everyone and so they understandably try everything:

• Re-offering the bottle repeatedly

• Following the baby's head with the nipple

• Walking or bouncing while feeding

• Distracting with toys or screens

• Trying again every few minutes

• Feeding whenever the baby is sleepy

• Encouraging just one more ounce

These strategies usually develop because parents are trying desperately to keep their baby nourished but it can become a double edged word. These strategies often work temporarily but if the baby has begun associating feeding with pain or stress, repeated pressure can unintentionally maintain or worsen the feeding conflict.

This is why treating reflux and treating feeding aversion are related—but not always the same thing.

Could the diagnosis itself be wrong?

Possibly.

This doesn't necessarily mean anyone made a mistake; infant symptoms overlap enormously. A young baby who cries, arches, sleeps poorly, spits up and struggles during feeds may initially appear to have reflux, but those behaviours aren't specific to GERD. As more information becomes available, the clinical picture can change.

When a baby doesn't respond as expected to treatment, good medical care includes being willing to ask:

Could we be dealing with something else?

Reconsidering a diagnosis isn't failure, it's an important part of clinical reasoning.

Should my baby be taking reflux medication long term?

This depends entirely on why the medication was prescribed and the baby's ongoing clinical needs.

Medication shouldn't simply continue indefinitely because it was started months earlier and babies grow and symptoms change, treatment should be periodically reassessed.

Questions may include:

Does this baby still need acid suppression?

Are the original symptoms still present?

Is the current dose appropriate?

Is there a plan for reassessment or eventual discontinuation?

For some babies, treatment may be needed for a period of time. For others, the indication may no longer be present. This decision should be made with the prescribing clinician.

Can I just stop my baby's reflux medication?

Don't abruptly stop or substantially change prescribed reflux medication without discussing it with your baby's healthcare provider.

After longer-term acid suppression, stopping certain medications suddenly can sometimes be followed by rebound acid hypersecretion, in which acid production temporarily increases. That can make symptoms appear to flare after discontinuation and can even mean that some children end up restarting the medication.

This doesn't necessarily mean the baby will need medication forever, but when medication is no longer required, the prescriber should recommend an appropriate discontinuation plan based on the medication, duration of treatment and individual baby.

When should I ask for the treatment plan to be reviewed?

It is reasonable to speak with your baby's healthcare provider if:

• There has been no meaningful improvement

• Symptoms initially improved and have returned

• Your baby has grown significantly since the medication was prescribed

• Feeding is becoming progressively more difficult

• Your baby appears to experience significant pain

• You suspect medication side effects

• Your baby only reliably feeds while sleepy or asleep

• Your baby is refusing increasing numbers of feeds

• You're unsure how or when the medication should be administered

• The medication has continued for a prolonged period without reassessment

• New symptoms have appeared

  
  

You don't necessarily need to ask:

“Can we increase the medication?”

A more useful question may be:

“Can we review whether this is still the right treatment plan?”

When do symptoms need urgent medical attention?

Not every concerning symptom should be attributed to reflux.

Seek prompt medical attention if your baby experiences symptoms such as:

• Difficulty breathing

• Blue, grey or unusually pale colour

• Significant choking or breathing difficulty during feeds

• Green or bile-stained vomiting

• Blood in vomit

• Repeated forceful or projectile vomiting

• Significant dehydration

• Marked lethargy or difficulty waking

• A markedly swollen or tender abdomen

• A baby who appears acutely unwell

Very young babies with fever also require appropriate medical assessment.

The goal isn't more medication. It's the right treatment.

When a baby continues to struggle despite reflux treatment, parents understandably want something to change.

Successful reflux management isn't about finding the highest dose or using the greatest number of medications, it's about understanding the problem and addressing it accordingly.

Sometimes the medication needs adjusting.

Sometimes the dose needs reviewing because the baby has grown.

Sometimes administration can be optimized.

Sometimes a different medication may be more appropriate.

Sometimes another gastrointestinal, feeding or swallowing problem needs investigation.

And sometimes the reflux pain has improved—but a feeding aversion that developed while feeding was painful still needs to be addressed.

The goal is to use medication thoughtfully, appropriately and effectively when it is indicated.

The right treatment for the right baby, for the right reason.

Is Your Baby Still Struggling Despite Reflux Treatment?

At Crying, Colic & Beyond, we work with families whose babies continue to experience reflux symptoms, discomfort or feeding difficulties despite previous treatment. Our telehealth consultations take a detailed look at the bigger picture—including your baby's symptoms, feeding history, growth, previous treatments, current medication and how it is being administered.

Rather than assuming persistent symptoms automatically require more medication, the goal is to understand why the current approach isn't producing the expected improvement and determine appropriate next steps.

For babies who have also developed bottle refusal, sleep feeding or other signs of feeding aversion, we can consider the medical and behavioural aspects of feeding together.

Learn more about our Reflux & Colic Consultation →

About Dr. Jennifer Harris

Dr. Jennifer Harris is a board-certified pediatrician with extensive experience working with infants and children experiencing reflux, gastrointestinal symptoms, feeding difficulties and feeding aversion.

Through Crying, Colic & Beyond, she works with families via telehealth using an individualized approach to understand not simply whether a baby has been diagnosed with reflux, but whether the current diagnosis and treatment plan adequately explain and address the child's symptoms.

This article is intended for general educational purposes only and does not constitute medical advice, diagnosis or treatment. Medication choice, dosing, administration and discontinuation should be determined by an appropriately qualified healthcare professional familiar with your baby's individual medical history. Never start, stop or change your baby's prescribed medication based solely on information in this article.