Purpose In this study, we aimed to describe the clinical characteristics, laboratory findings, aetiologies, and role of PCR in the decision on the management plan and duration of hospital stay in Jordanian children diagnosed with aseptic meningitis. Methods This retrospective observational cohort study included children diagnosed with meningitis who were admitted to the paediatric ward at Jordan University Hospital (JUH) during the period from January 2016 to August 2020. Patients were identified through the ICD9 discharge code of meningitis. Patients diagnosed with aseptic meningitis (defined as a patient with signs and symptoms of meningitis with a cerebrospinal fluid (CSF) white cell count of >5 cells/mm 3 , and a negative CSF Gram stain) were included, while patients who had low CSF glucose (<50% of serum) positive cerebrospinal fluid Gram stain and/or culture for bacterial meningitis were excluded. Files were reviewed to collect data on the clinical picture, viruses identified by the CSF viral polymerase chain reaction (PCR) panel, duration of medication, and hospital stay in patients with identified virus versus those with negative viral PCR. Results One hundred and thirty-one patients were included: 87 males (66.4%) and 44 females (33.5%). Fever was the most common presenting symptom, followed by headache, vomiting, and excessive sleep in 48.0%, 42.7%, and 35.8% of the patients, respectively. Prior oral antibiotic use was reported in 48/125 (38.4%) patients. White blood cell count (WBC) ranged from 4.800 to 22.000. cells/mL, 45 patients (34.3%) had counts above 15.000 cells/mL. C-reactive protein level was high in 61/103 (59.2%) patients. CSF WBC count was <100 in 62 (47.3%) patients while neutrophils predominance of >70% was present in 27 (20.6%) patients. Viral panel PCR was done for 100/131 (76.3%) patients and was positive in 66/100 (66%) patients; with enterovirus being the most common identified viruses (60/100; 60%). The average duration of hospital stay was 5.9 and 5.5 days for those with negative and positive PCR respectively. Ten (7.6%) patients had seizures upon presentation. None of the patients had any neurological sequel related to his meningitis. Conclusion Enteroviruses are the most common identified cause of paediatric aseptic meningitis in Jordan. Although PCR revealed an identified virus in around half of the patients, nevertheless, there was no adjustment in the management plan regarding duration of empirical antibiotic use and hospital stay. Increasing knowledge and awareness among clinicians on viral meningitis’ lab characteristics might have great impact on duration of hospital stay and thus would be reflected on the patient and the healthcare system as well.