© 2021. Thieme. All rights reserved.Objective The most common childhood convulsive disorder happens to be febrile seizure (FS), which is an important health problem leading to economic burden and parental anxiety. Further investigation into the etiological causes of FS will guide us for appropriate measures during the follow-up period. The aim of study was to identify the percentage of viral and bacterial pathogens in the etiological causes of children with FS, and also if there is any difference between simple and complex FSs. Methods This prospective study randomly enrolled 100 pediatric patients with FS between January 2017 and July 2017. Nasopharyngeal swabs were obtained from all children at presentation. The respiratory panel was performed with a multiplex real-time polymerase chain reaction method to detect the 21 most common viruses. A complete blood count, absolute neutrophil count, absolute lymphocyte count, C-reactive protein, erythrocyte sedimentation rate, procalcitonin, blood culture, throat culture, urine analyses, urinary culture, and stool tests analysis were performed in all the patients. Results During the study period, at least one virus was detected in 87% of patients. Bacterial agents were detected in only 13% of patients. Coinfections of the viruses and bacterial pathogens were found in 24% of patients. The most frequently detected virus was influenza A (Inf A) (18%), followed by rhinovirus (12%). Coinfections of the viruses and bacterial pathogens, mixed viral infections, and Inf A were common in children who experienced complex FS. Inf A was detected in 16% of patients with simple FSs and 30% of patients with complex FSs and a significant difference between them (p < 0.01). Conclusion The results of this study showed that respiratory viral and bacterial pathogens are important in the etiology of FS in children. It is considered that complex FSs may be triggered by Inf A. The fact is viral pathogens are very common; therefore, antibiotics must be carefully prescribed. These results also draw attention to the use of the quadrivalent influenza vaccine in the prevention of FS related to the flu.