Abstract Background The frequency of false negatives in exercise provocation tests (EPTs) when evaluating exercise‐induced allergic reactions on desensitization (EIARD) remains unclear. This study aimed to determine the frequency of allergic symptom induction after a negative EPT result in patients at risk of EIARD and to identify its associated factors. Methods This retrospective cohort study analyzed 109 patients aged 5–18 years who underwent EPTs between February 2012 and March 2023 to assess EIARD after wheat oral immunotherapy (OIT). EPT was performed in all cases after rush OIT and in high‐risk cases after slow OIT. Patients with a negative/indeterminate EPT result were monitored for 1 year. Individuals who developed allergic reactions during exercise after wheat ingestion were categorized as “Event+” and were regarded as having false‐negative EPT results. Patients without events were categorized as “Event−”. Candidate factors between the Event+ and Event− groups were compared using nonparametric statistical tests. Results Among 53 patients with negative/indeterminate EPT results, 14 (26.4%) experienced allergic symptoms during follow‐up (Event+ group). Higher ω5‐gliadin‐specific IgE levels at the time of EPT were significantly associated with Event+. No other factors (i.e., age, sex, allergy severity, or exercise intensity) showed any association. All Event+ cases occurred outdoors, suggesting a possible influence of environmental factors. Conclusion False negatives occurred in 26.4% of pediatric wheat‐desensitized patients with EPTs. Our findings highlight the need to periodically monitor EIARD after negative EPT results. Future studies should explore methods to improve the accuracy of EPTs and identify predictive markers of EIARD risk.