Acute otitis media (AOM) is one of the most common infectious diseases in pediatric clinical facilities and has a significant impact on health care. It is a polymicrobial disease and is usually preceded by a viral upper respiratory tract infection. Data on the spectrum of viruses that cause AOM in Indonesia are still limited. This study analyzed nasopharynx (NP) samples collected from 119 school children with AOM in Banyumas Regency, Central Java, Indonesia. Viral RNA was extracted for cDNA synthesis, followed by PCR and sequencing tools for detection of a panel of respiratory viruses using family-level primers for Coronaviridae, Enterovirus, Bocavirus, and Pneumovirinae for bocavirus. In total, 37 out of 119 NP samples (31.1%) tested positive for viruses. Human rhinovirus B was the predominant virus identified (32.4%) followed by rhinovirus C (29.7%), human rhinovirus A (27%), and human bocavirus (5.4%). Rhinovirus are predominant viral pathogens within school children with AOM in Central Java, Indonesia.