Background: Influenza is a commonly encountered respiratory tract infection and diagnosis remains to be a challenge. Use of a rapid antigen test may influence decisions on treatment in the emergency room (ER). Objectives: This research aims to determine the effects of rapid influenza antigen test (RIAT) on antimicrobial management of influenza-like illness (ILI) in the ER, determine the clinical profile of pediatric patients with ILI and look into the relationship between RIAT result, symptomatology, and immunization status. Methods: This is a cross-sectional study which involved review of charts of 195 pediatric patients with ILI who underwent RIAT (KlintecTM) through a nasopharyngeal swab in the ER of a tertiary hospital from September 2019 to February 2020. Chi-square, Fischer exact test and likelihood ratio were used for data analysis. Results: Most pediatric patients were 7–12 years old males. Majority presented with fever, cough, and colds and underwent RIAT at 2–4 days from onset of illness. About 73.33% of study participants did not receive their yearly influenza vaccine and 70.7% of patients with positive RIAT had no influenza vaccine. There is a lower percentage of vaccinated children who developed cough (86.5% vs. 89.5%) and colds (80.8% vs. 83.2%) when compared with unvaccinated children. RIAT result significantly affected management in terms of antimicrobial prescribing to patients with ILI. Conclusion: Influenza presents with non-specific symptoms and vaccination remains a major preventive measure against the disease. The result of RIAT facilitates targeted treatment for influenza and decreases unnecessary antibacterial use, but this should be done with careful thought and interpretation.