Young people frequently use and access prescribed medications for a range of health problems. Medications aimed at treating both common health problems and long-term physical and mental health needs in adolescence can have a significant effect on a young person’s emotional well-being. We use a series of case studies to illustrate the challenges for healthcare professionals supporting young people with medication use. The studies illustrate the efficacy and limitations of medication on improving emotional well-being by alleviating illness and distress, and how this efficacy must be balanced against both the adverse effects and the burden of treatment. There are specific challenges for medication management during adolescence including issues of adherence/concordance, facilitating autonomy and participation in decision making, and promoting independence.