Medication non-adherence among youth with chronic health conditions is a healthcare crisis in the United States. Nearly 20% of youth experience a chronic illness, yet most do not comply with their treatment regimen. Various challenges to adherence arise, such as not understanding the purpose of treatment, painful or difficult administration, forgetfulness, and mood disorders such as anxiety. Cognitive behavioral therapy (CBT) is an empirically supported approach to increasing treatment adherence. Modular CBT incorporates psychoeducation, cognitive restructuring, and behavioral experiments to promote better disease management. This article focuses on the application of CBT to four medical conditions characterized by elevated levels of non-adherence: pill-swallowing difficulties, asthma, type 1 diabetes, and inflammatory bowel disease in youth. The review integrates findings on contextual issues (e.g., ethnocultural variations, the impact of the COVID-19 pandemic), research on non-adherence, and CBT outcome studies. Additionally, limitations of the existing literature and training recommendations are provided.