Previous cross-sectional based research suggests that students' perceptions of the learning environment are associated with emotional and behavioural problems (EBP). However, it is not clear to what extent the associations identified are merely reflections of individual student characteristics. The present study explored this issue by utilizing a pre-test post-test design to minimize the influence of stable individual characteristics on associations of perceived learning environment with EBP. By conducting the study in a Norwegian secondary school implementing relatively substantial changes in the learning environment we explored how changes in students' perceptions of the learning environment were related to changes in reports of EBP. Results suggest that associations between learning environment factors and EBP are not merely reflections of individual characteristics. Changes in EBP were significantly related to changes in most of the learning environment factors.