Most children infected with the SARS-CoV-2 virus have asymptomatic or mild disease with a short clinical course and excellent outcome; meanwhile, some children experienced persisting symptoms lasting > 12 weeks from the COVID-19 infection diagnosis. This study aimed to define the acute clinical course of SARS-CoV-2 virus infection and outcomes in children after recovery. This prospective cohort study was conducted on 105 children (aged < 16 years) with confirmed COVID-19 infection at Jamal Ahmed Rashid Teaching Hospital, Sulaimaniyah, Iraq, from July to September 2021. The symptomatic and suspicious cases of COVID-19 infection in children were confirmed by real-time reverse transcriptase-polymerase chain reaction (RT-PCR) on nasopharyngeal swabs. About 85.6% of children fully recovered at ≤ 4 weeks from initial COVID-19 infection diagnosis, 42% were hospitalized, while 15.2% reported long COVID-19 infection symptoms. The most commonly reported symptoms were fatigue (7.1%), hair fall (4.0%), lack of concentration (3.0%), and abdominal pain (2.0%). Children aged 11–16 showed a greater risk of long-term COVID-19 infection symptoms. We also observed a higher risk of long COVID infection symptoms in those who reported ongoing symptoms at 4–6 weeks of follow-up assessment (p= 0.01). Despite mild disease and complete recovery in most children, many suffered from long COVID infection symptoms.