Children experience nausea, regurgitation, vomiting, abdominal pain and a burning feeling similar to acid reflux (heartburn). They may have difficulty swallowing and gag frequently. Often, they feel like something is stuck in their throat. This is called dysphagia. If EoE goes untreated, the esophagus may narrow because of scarring. This is called stricture.

Infants with EoE don't want to breastfeed or take a bottle, and may frequently spit up and arch the back - a sign of pain. Older children eat reluctantly and slowly, don't grow as quickly as expected, develop seemingly irrational aversions to certain foods, and may have trouble sleeping. They may complain of heartburn and dysphagia. Sometimes EoE is diagnosed after a child or teenager comes to the hospital with food in the esophagus that he or she is unable to cough up. This is called food impaction.

EoE shares many symptoms with acid reflux, so a doctor will first prescribe an acid blocker medication or proton pump inhibitor (PPI). These medicines do not help EoE, so if symptoms persist, the doctor will know reflux isn't the cause. It's estimated that up to 10 percent of children with reflux have EoE.