Till date, there is paucity of published literature on clinical manifestations of Coronavirus disease 2019 (COVID-19) in children from low-middle-income countries (LMIC). Most of the reports are from Europe, USA or China. Our study aimed to capture data on varied and unusual clinical presentation and management of MIS-C (Multisystem Inflammatory Syndrome in Children) with COVID-19 and compare the MIS-C and non-MIS-C children. This was a single-centre cohort study of 41 COVID positive children 0–12 years age hospitalized between 1 April 2020 and 31 July 2020. Data were entered into standardized WHO Case Report Form and analysed using strata 15.0 statistical software. Twenty out of 41 children fulfilled the criteria of MIS-C. Male-to-female ratio in the cohort was 1.73:1. In MIS-C cases, predominant clinical manifestation was fever (100%), neurological manifestations (80%), lower respiratory tract infection (50%), rash (35%) and acute gastroenteritis (25%). They were categorized into Acute Encephalitis-like illness in 35%, Kawasaki-like disease, Toxic Shock-like syndrome and Comorbidity with systemic complications in 20% each. Ninety percent of MIS-C cases required oxygen supplementation with odds ratio (OR) 18 (3.22–100.48), whereas 65% required mechanical ventilation with OR 37.14 (4.08–338.10). Most of them had raised inflammatory markers and hepatic enzymes derangement. Steroids, Intravenous immunoglobulin and supportive therapy were mainstay of management for MIS-C group. Most MIS-C group children had multisystem involvement with predominant neurological manifestations at time of presentation. Delay in diagnosis and referral may have adversely affected the prognosis and outcome.