Background Strategies to mitigate the impact of COVID‐19 in special populations are complex and challenging. Few studies have addressed the impact of COVID‐19 on pediatric patients with cancer in low‐ and middle‐income countries. Methods Multicenter observational cohort study with prospective records and retrospective analyses starting in April 2020 in 21 pediatric oncology centers distributed throughout Brazil. Participants: Patients under 18 years of age who are infected by the SARS‐CoV‐2 virus (confirmed diagnosis through reverse transcriptase‐polymerase chain reaction [RT‐PCR]) while under treatment at pediatric oncology centers. The variables of interest included clinical symptoms, diagnostic and therapeutic measures. The repercussions of SARS‐CoV‐2 infection on cancer treatment and general prognosis were monitored. Results One hundred seventy‐nine patients were included (median age 6 [4–13] years, 58% male). Of these, 55.9% had acute leukemia and 34.1% had solid tumors. The presence of SARS‐CoV‐2 was diagnosed by RT‐PCR. Various laboratory markers were analyzed, but showed no correlation with outcome. Children with low or high BMI for age had lower overall survival (71.4% and 82.6%, respectively) than those with age‐appropriate BMI (92.7%) ( p = .007). The severity of presentation at diagnosis was significantly associated with outcome ( p < .001). Overall mortality in the presence of infection was 12.3% ( n = 22). Conclusion In children with cancer and COVID‐19, lower BMI was associated with worse prognosis. The mortality in this group of patients (12.3%) was significantly higher than that described in the pediatric population overall (∼1%).