Background and aims: To assess clinical outcomes and quality of life (QoL) of children, adolescents, and young adults (C-AYAs) with chordomas (CH) or chondrosarcomas (CS) after pencil beam scanning proton therapy (pbsPT). Methods: Seventy-six C-AYAs treated between 1999-2023 were included. Median age was 16.6 years (1.5-25.4). Forty-four (57.9%) were AYAs (15-25 years). Most tumors were CHs (n=49; 64.5%) and located in the skull-base (68.4%). Median radiation dose was 73.8 Gy (RBE) (54-75.6). Twenty-six (34.2%) patients underwent complete resection. PEDQOL questionnaire was used to assess QoL. Kaplan–Meier and log-rank test were used for the analysis. Results: With a median follow-up of 88.4 months (range, 1.8 – 257.6), 9 (11.8%) patients died. Local failure only developed in 9 (11.8%) patients. Two (2.6%) presented with distant failure only and another (1.3%) had both. Seven-years overall survival (OS), local control (LC), and distant control (DC) were 86.3%, 87.7% and 95.7%, respectively. Children when compared to AYAs had worse 7-years DC (90% vs. 100%, p=0.049). Surgical resection vs. biopsy was associated with better 7-years LC (87.1% vs. 67.7%, p=0.031). Recurrent tumors showed worse OS, LC, and DC (94.5% vs. 44.6%, p<0.001; 93.2% vs. 36.6%, p<0.001; 98.3% vs 77.6%, p=0.003). Seven-years freedom from grade ≥3 late toxicity was 83.1%. Three (3.9%) children with CH developed secondary tumors. QoL did not differ from a healthy cohort 2 years after pbsPT. Conclusions: Excellent clinical outcomes with acceptable long-term toxicity and QoL were observed for C-AYAs with CH/CS after pbsPT. Recurrent tumors, children, and lack of surgical resection was associated with worse prognosis.