During the early stage of coronavirus disease 2019 (COVID-19) pandemic, detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was a priority; however, influenza viruses and RSV continued to cause seasonal epidemics complicating the diagnostic strategies. In the present study we estimated the proportion of SARS-CoV-2-negative pediatric cases attributed to respiratory syncytial virus (RSV) and influenza viruses during a 3-month period after the identification of the first COVID-19 case in Greece. Ninety SARS-CoV-2-negative children hospitalized with acute respiratory tract infection were included in the study. Following a SARS-CoV-2 negative result, the samples were tested by molecular methods for detection of RSV and influenza viruses. The positive samples were further tested for identification of the subtype of the viruses. We detected RSV or influenza viruses in 22 (24.4%) samples. Influenza virus was detected in 13 (14.4%) patients (two of type A and 11 of type B), and RSV (all RSV-A) was detected in 9 (10%) patients. In conclusion, a syndromic approach for simultaneous detection of at least influenza virus, SARS-CoV-2 and RSV will be beneficial for the prompt implementation of appropriate hospital management including antiviral treatment and isolation measures.