Educational transitions are associated with significant changes. If students cannot overcome these challenges, their well-being and motivation may be impaired. Students with clinically relevant emotional or behavioural disorders (EBDs) are at risk for negative transitional experiences. We conducted a systematic review summarising transitional outcomes of students with EBDs. After an electronic search in eight scientific databases, 4,930 publications were screened against six inclusion criteria. Two coders assessed the eligibility of 181 full-texts. We included k = 22 studies published in English or German (1988-2017). Students with autism (k = 15) and transitions out of school (k = 13) were examined most frequently. Well-being, achievements, social participation, support and expectations were observed. Poor well-being and social difficulties were prevalent, but often adjusted over time. The results are limited by the inclusion criteria and search procedures. Nevertheless, the review closes a research gap and has implications for the implementation of interventions and a supportive transition environment for students with clinically relevant EBDs. Further research on individual changes and supportive approaches during transitions is needed.