Abstract Background: There is scarcity of data summarizing the clinical picture, laboratory, and imaging findings as well as outcome in children with malignancy and Covid-19 infection. This study characterizes a detailed comparison of pediatric oncology patients with and without Covid infection. Methods: This is a retrospective study conducted from March 2020-June 2020 at The Indus hospital, Karachi, Pakistan. Pediatric oncology patients (1 month-18 years) with and without covid infection were included in the study. Clinical presentation, laboratory and imaging findings, disease severity and outcome was compared between both cohorts. Results: The mean age of children with and without Covid, was 8.0 ± 4.9 years and 7.4 ± 4.1years respectively. Hematological malignancy comprises the largest number of patients followed by solid tumours. Lymphocytosis and low NLR is observed in covid positive group. Cardiac dysfunction (1.4% vs 0), ARDS (8%vs 0) and lower SpO2/FiO2 ratio (473 vs486) found to be associated with severe disease in covid positive group (p-value<0.05). Overall mortality in children with covid was 6.8% versus 2.7% in children without covid. Conclusion: Pediatric patients with malignancy have different clinical features and laboratory parameters as compare to children without malignancy. ARDS, absolute lymphocytosis and low NLR is associated with severe disease in children with malignancy and covid infection. In contrast to adults, biochemical markers and CBC parameters are not helpful in recognizing covid infection in pediatric patients with malignancy.