Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma of childhood with 250-350 cases diagnosed annually in the United States. Biliary tract rhabdomyosarcoma is rare, representing <1% of the RMS cases. Due to its location, resection is clinically challenging, and functional complications exist and persist from biliary obstruction. The anatomical location of this tumor presents both opportunities and challenges for pencil beam scanning proton therapy. Proton therapy offers a dosimetric and clinical advantage by sparing the healthy liver, stomach, contra-lateral kidney and bowel. Motion management and anatomical variations, such as intestinal filling or weight loss, requiring routine dosimetric evaluation and possible adaptive treatment planning, present challenges for the use of proton therapy. By taking advantage of the superior dose distribution of proton radiation, assessing the impact of tumor and anatomy motion, and performing regular dose evaluations, biliary tract RMS is an ideal diagnosis for pencil beam scanning proton therapy.