Background: Stress ulcer prophylaxis is the considered standard of care in many critically ill patients in the intensive care unit (ICU). Whether there is overall benefit or harm of stress ulcer prophylaxis in critically ill children is unknown. Accordingly, we aim to assess patient-important benefits and harms of stress ulcer prophylaxis versus placebo or no treatment in critically ill children in the ICU. Methods/design: We will conduct a systematic review of randomized clinical trials with meta-analysis and trial sequential analysis and assess the use of proton pump inhibitors (PPIs) or histamine-2-receptor antagonists (H2RAs) versus placebo or no prophylaxis. We will systematically search the Cochrane Library, MEDLINE, EMBASE, Science Citation Index, BIOSIS, and Epistemonikos for relevant literature. We will follow the recommendations by the Cochrane Collaboration and the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement. The risk of systematic errors (bias) and random errors will be assessed, and the overall quality of evidence will be evaluated according to the Grading of Recommendations Assessment, Development, and Evaluation (GRADE) approach. Discussion: There is a need for an updated systematic review to summarize the benefits and harms of stress ulcer prophylaxis in critically ill children to inform practice and future research.