There is a large body of research exploring the difficulties young people experience on the transition to secondary education. However, there has been little comparative research yielding insights into how these experiences vary by institutional context. This article explores differences in school transition difficulties among young people in Scotland and Ireland using nationally representative longitudinal datasets -- Growing Up in Ireland and Growing Up in Scotland. Despite generally making the transition with most or all of their friends, transition difficulties are greater on average in Scotland than in Ireland, perhaps reflecting the shorter duration of primary education in Scotland. In both systems, young people coming from households with lower levels of income and education experience greater difficulties and this gap is only partially accounted for by school experiences at primary and secondary level. An interesting feature is contrasting gender patterns in the two systems, with boys experiencing more difficulties in Scotland and girls more adjustment problems in Ireland. The male disadvantage in Scotland is partly explained by school experiences; the female disadvantage in Ireland is related to more negative attitudes to Maths at primary level than boys. Vocabulary development in middle childhood plays a stronger role in influencing ease of transition in Ireland, most likely because of the large number of (literacy-based) subjects students take on entry to secondary school. The article points to the potential for further comparative research on school transitions to better understand the dynamics in different contexts.