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Background Post-COVID-19 changes in respiratory viral circulation may influence febrile seizures (FS) presentation, but associations between viral detection, co-detection and outcomes remain unclear. We evaluated associations between respiratory viral detection and clinical outcomes in children.Methods We retrospectively analysed children aged 6–60 months with FS who underwent multiplex respiratory virus reverse transcriptase-PCR (RT-PCR) in a tertiary paediatric emergency department between April 2023 and March 2025. Logistic regression assessed the associations of individual viruses and viral co-detection (≥2 viruses) with the risks of complex febrile seizures (CFS) and hospitalisation, adjusting for covariates (age, sex, season, Korean Triage and Acuity Scale, mental status, body temperature, peripheral oxygen saturation and family history).Results Among 558 children, 95 (17.0%) had CFS. Parainfluenza virus (PIV) (adjusted OR 0.38, 95% CI 0.16 to 0.89) and seasonal coronaviruses (adjusted OR 0.33, 95% CI 0.12 to 0.89) were associated with lower odds of CFS. PIV (adjusted OR 0.37, 95% CI 0.17 to 0.80) and respiratory syncytial virus (adjusted OR 0.32, 95% CI 0.13 to 0.78) were associated with lower odds of hospitalisation. Viral co-detection occurred in 47.8%, and each additional virus was associated with lower odds of CFS (OR 0.62, 95% CI 0.44 to 0.88) and hospitalisation (OR 0.66, 95% CI 0.49 to 0.90).Conclusions Detection of certain respiratory viruses and viral co-detection was associated with lower odds of CFS and hospitalisation. Viral co-detection did not uniformly indicate greater severity in FS, supporting cautious interpretation of multiplex RT-PCR results. Residual confounding and selection bias related to the retrospective design and clinician-directed testing should be considered.