Introduction: Children and adolescents with cancer report increased fatigue and decreased physical activity, introducing risk factors for chronic disease and suppressed quality of life. Research suggests an inverse relationship between fatigue and physical activity, but the biological explanation is not well understood. The purpose of this study was to 1) explore metabolites associated with fatigue or physical activity and 2) to identify any shared metabolomic elements. Methods: Children, ages 8-17 years, attending a pediatric oncology summer camp provided Patient-Reported Outcome Measurement System® (PROMIS) Pediatric Fatigue assessments, physical activity data (steps/day), and urine samples pre- and post-camp. Differences in PROMIS Pediatric Fatigue scores and average daily steps were calculated using paired t-tests. Liquid chromatography-tandem mass spectrometry was conducted using a targeted metabolomic approach. Results: Thirty-two enrolled children had complete data. Fatigue scores decreased (pre-camp 45.1; post-camp 42.1; p = 0.04) while steps-per-day increased (pre-camp 6699; post-camp 16,021; p < 0.001). Twenty-seven metabolites significantly differentiated (false discovery rate <0.20) between low, medium, or high physical activity, while 8 metabolites discriminated between high and low fatigue. Indole-3-lactic acid, a tryptophan metabolite, was significantly associated with both physical activity and fatigue. Conclusion: This study provides evidence of metabolome associations with fatigue and physical activity in children with cancer. Overlapping metabolomic elements provide evidence of biological inter-connectivity and suggest areas for future research. Given the known evidence regarding the benefits of physical activity, and the potential interaction with fatigue, nurses should routinely assess patient reports of these elements and provide patient/family education related to fatigue management and physical activity goals.