Pediatric oncology patients are at high risk of developing clinical deterioration and organ dysfunction during their illness. Heart rate variability (HRV) measured using electrocardiography waveforms is associated with increased organ dysfunction and clinical deterioration in adult and pediatric patients in the intensive care unit (ICU). Here, we explore the feasibility of using photoplethysmography (PPG)-derived integer pulse rate variability (PRVi) to estimate HRV and determine its association with organ dysfunction in pediatric oncology patients in the ward and pediatric ICU. The advantage of using PPG sensor data over electrocardiography is its higher availability in most healthcare settings and in wearable technology. In a cohort of 38 patients, reduced median daily PRVi was significantly associated with increase in two pediatric organ dysfunction scores after adjusting for confounders (p < 0.001). PRVi shows promise as a real-time physiologic marker of clinical deterioration using highly-available PPG data, but further research is warranted.