We investigated trends in associations between physical and social neighbourhood and school characteristics and adolescent mental health problems between 2005 and 2017. Nationally representative, repeated cross-sectional data collected in the Netherlands among primary (N = 5,871) and secondary school students (N = 20,778) were analysed through cross-classified multilevel models. Hardly any evidence was found for over-time changes in associations between neighbourhood and school characteristics and adolescent mental health problems. Findings showed that for both groups of students, only social characteristics within the two contexts were associated with adolescent mental health problems. For secondary school students, school effects were larger than neighbourhood effects, while the opposite was true for primary school students. Specifically, primary school students residing in more socially fragmented or lower socioeconomic status (SES) neighbourhoods, and lower SES schools, reported more conduct problems and peer relationship problems. For secondary school students, only the SES of the neighbourhood and the school was associated with all four aspects of mental health problems. Remarkably, the direction of the associations between neighbourhood/ school SES and adolescent mental health problems varied across the different mental health outcomes. More research is warranted to replicate our findings.