Background: Febrile seizures are the most common pediatric seizure disorder, often triggered by viral infections, particularly respiratory viruses. This study aims to determine the frequency and spectrum of respiratory pathogens in children with febrile seizures and to identify clinical predictors of respiratory pathogen detection, with a focus on influenza. Methods: We prospectively recruited 243 children aged 6 months to 6 years hospitalized for febrile seizures at a Malaysian tertiary hospital between April to December 2024. Nasopharyngeal swabs were tested using a multiplex respiratory panel (RP) PCR for 23 respiratory pathogens. Clinical characteristics were compared between respiratory panel (RP)-positive and RP-negative cases. Two multivariate logistic regression analyses were performed: the first identified predictors of RP positivity, and the second identified predictors of influenza among RP-positive cases. Results: Respiratory pathogens were detected in 70.8% of febrile seizure cases, with influenza A (22.2%), rhinovirus/enterovirus (16.0%), SARS-CoV-2 (6.2%) and influenza B (5.3%) being the most common pathogens identified. Multivariate analysis identified cough as an independent predictor of RP positivity (aOR 2.79, 95% CI 1.14–6.81, p=0.024). Among RP-positive cases, recent sick contact (aOR 5.57, 95% CI 1.99–15.54, p=0.001) and lymphopenia (aOR 2.90, 95% CI 1.14–7.39, p=0.026) were independent predictors of influenza. Conclusion: Respiratory viruses were frequently detected in febrile seizures, with influenza being a major contributor. While routine testing is unnecessary, a targeted approach based on these clinical predictors could improve diagnostic accuracy, facilitate early antiviral treatment and reduce unnecessary antibiotic prescriptions.