Primary–secondary school transition encompasses multiple social, academic and environmental changes which can negatively impact children’s emotional well-being. Children with Social, Emotional and Mental Health difficulties (SEMH) are believed to be especially vulnerable during this time. However, the voices of children with SEMH are heavily underrepresented in this field within practice and research. The present case study examined how children with SEMH difficulties within one special school experience primary–secondary school transition and how they are supported, in order to make recommendations to improve this period. The case study was qualitative and longitudinal, conducted over 18-months and methodologies included ethnographic observations, child photo-elicitation focus groups (with 11 Year 6 children) and three adult interviews. Findings demonstrated that over primary–secondary school transition children with SEMH difficulties (a) negotiate significant structural changes in support (often unanticipated) and (b) need to feel a sense of safety and belonging. To manage this effectively, transition provision for children with SEMH difficulties needs to consider their short-term emotional well-being whilst still in primary school, in addition to their long-term well-being looking ahead to secondary school. Greater collaboration and communication across schools and stakeholders can help ensure children receive continuity in standards and support.