Background: Most children and adolescents diagnosed with cancer become long-term survivors. For most of them, regular follow-up examinations to detect and treat late effects are necessary, especially in adulthood. The transition from pediatric to adult-focused follow-up care is a critical moment for childhood cancer survivors (CCSs); a substantial proportion of CCSs are lost to follow-up in this transition process and do not attend follow-up care in adulthood. This can have serious effects on survivors’ health if late effects are not discovered in a timely fashion. Objective: In this study, we primarily assess the current follow-up situation, related needs, and knowledge of adolescent and young adult CCSs who have transitioned from pediatric to adult-focused follow-up care. As secondary objectives, we evaluate transition readiness, identify facilitating factors of transition and adherence to long-term follow-up (LTFU) care, and compare three different transition models. Methods: The Aftercare of Childhood Cancer Survivors (ACCS) Switzerland study is a prospective, multicenter, observational study that was approved by the ethics committee in February 2019. We are recruiting CCSs from three pediatric oncology centers and using questionnaires to answer the study questions. Results: To date, we have recruited 58 participants. The study is ongoing, and recruitment of participants will continue until January 2021. Conclusions: The ACCS study will provide information on CCSs’ preferences and expectations for follow-up care and their transition into the adult setting. The results will help improve the LTFU care and cancer knowledge of CCSs and subsequently enhance adherence to follow-up care and reduce loss to follow-up in adulthood. Trial Registration: ClinicalTrials.gov NCT04284189; https://clinicaltrials.gov/ct2/show/NCT04284189?id=NCT04284189 [JMIR Res Protoc 2020;9(8):e18898]