In recent years, the prevalence of laryngopharyngeal reflux has risen, especially among pediatric patients. The diagnosis of laryngopharyngeal reflux relies on patient history and clinical assessment using the Reflux Finding Score and Reflux Symptom Index as crucial diagnostic tools. Some studies have proposed a link between pepsin and laryngopharyngeal reflux, potentially triggering palatine tonsil hypertrophy. Our study aimed to investigate the correlation between laryngeal and pharyngeal manifestations of laryngopharyngeal reflux through two questionnaires and the presence of pepsin in saliva and palatine tonsils in a pediatric population. Pepsin in saliva was detected using a Western blot method, while immunohistochemistry assessed its presence in palatine tonsils. Although no statistically significant differences in Reflux Finding Score and Reflux Symptom Index were found between the immunohistochemistry-positive (IHC-positive) and immunohistochemistry-negative (IHC-negative) groups, median reflux symptom index and Reflux Finding Score values consistently trended higher in the IHC-positive group. This suggests a potential connection between elevated index values and pepsin presence in tonsillar tissue. Further investigations are essential to fully comprehend the clinical implications of these findings.