A range of long-term neurological conditions may be diagnosed in young adulthood. These conditions are generally not curable, and most people need to take ongoing treatment for symptom control and/or disease modification. When chronic diseases are diagnosed before people have completed their families, there is a need to balance the potential benefits of treatment for the mother against potential risk(s) to the fetus from exposure to medications during pregnancy. Whilst available data regarding short-term fetal outcomes following treatment exposures during pregnancy is rapidly increasing, information regarding longer-term outcomes is more limited. The association of fetal exposure to valproate with serious long-term neurodevelopmental outcomes has highlighted the importance of capturing and evaluating long-term data. In this review we examine available evidence around the long-term effects of treatments used for the most common long-term neurological conditions diagnosed in early adulthood, namely epilepsy, migraine and neuroinflammatory disorders. We draw from existing literature across a range of diseases and discuss strategies to improve future knowledge.