Background In oncology, pharmacists contribute to safety and effectiveness of drug treatment, identifying, preventing and forwarding solutions to drug-related problems (DRPs). However, it is still necessary to elucidate the profile of drug-related problems in pediatric cancer treatment to contribute to guide clinical pharmacy activities. Methods A retrospective cross-sectional study was conducted. Records on Excel® spreadsheets of 2 years of pharmaceutical assistance were analyzed regarding the prescriptions of chemotherapy for hospitalized patients aged 0–19 years. Data on age, sex, cancer diagnosis, protocol and drugs prescribed were collected. Causes and types of DRPs and pharmacists’ interventions as their rate of acceptance were measured according to PCNE V 9.0. Results Drug-related problems were identified for 84 patients, in 5.3% of analyzed prescriptions. Leukemias, patients aged 0–4 years and male sex were associated with higher rates of drug-related problems. The BFM 2009 protocol for acute lymphocytic leukemia treatment had the highest frequency of prescriptions with drug-related problems. Main drug-related problems were related to effectiveness (49.2%) and safety (33.2%), with most of them due to drug selection and dose. Rate of acceptance of interventions was 92.2% and 90.6% of drug-related problems were fully resolved. Mercaptopurine and filgrastim were the drugs most associated with drug-related problems. Oral antineoplastic agents represented 36% of the prescriptions with drug-related problems. Conclusion The high rate of acceptance of pharmacist interventions demonstrates the relevance of the pharmacist participation in the care of hospitalized pediatric patients undergoing chemotherapy. Pharmacists need to take attention to cases of necessity of drug prescription, intervening with other health professionals. Special attention to oral chemotherapy is required.