Background Given the poor prognoses and potential treatment toxicities faced by pediatric patients in early-phase oncology trials, evaluating quality of life (QoL) is crucial for both families and physicians when considering patient recruitment. This prospective, longitudinal study evaluates the impact of trial participation on QoL in children, agreement between self-reports, proxy-reports, and physician assessments, and associations with demographic and clinical factors. Procedure Patients aged 5–18 years enrolled in phase I/II clinical trials at Hospital Niño Jesus from 2019 to 2023 and their caregiver proxies were eligible. PedsQL 3.0 Cancer Module was independently completed by children and proxies at baseline, day +30, and day +90 of cycle 1 day 1. Stratified analyses by gender, age, tumor type, outcome, reason of end of treatment, and trial characteristics were performed. Agreement between child, proxy, and investigator responses was measured. Results Ninety-three pediatric patients with cancer and their proxies were included. The 38.71% of patients and 33.33% of proxies experienced a clinically relevant change in QoL scores after 30 days. Patients in phase II trials demonstrated greater QoL improvements compared to phase I (p = 0.0061). No significant associations were found between improvement of QoL and demographic or clinical factors. Proxies consistently reported lower QoL scores than patients, while physicians underestimated symptom severity compared to patient-reported outcomes. Conclusions Trial participation aligns with maintaining or improving QoL, particularly in later-phase trials. Discrepancies among patient, proxy, and investigator perspectives underscore the necessity of multi-informant tools to capture comprehensive insights.