AIM: Little is known about the association between school experiences and mental health in young schoolchildren. This study explored the cross-sectional and prospective associations between children’s school experiences and mental health in middle childhood. METHODS: We gathered comprehensive population-based data on the school experiences and mental health of 592 schoolchildren attending grades three and six in Sweden (ages approximately nine and 12 years). The KIDSCREEN questionnaire was used to measure school experiences in both age groups while the Child Behavior Checklist and the Strengths and Difficulties Questionnaire measured mental health in grades three and six, respectively. RESULTS: Children with problematic school experiences in grade three had an approximately two times higher odds for concurrent total, internalised, externalised, attention-hyperactivity and social problems. They also had a 1.5-2.5 higher odds for these mental health problems three years later. Likewise, there was an association between problematic school experiences in grade three and lower levels of prosocial behaviour three years later. These associations were shown in both boys and girls, but were particularly pronounced in girls. CONCLUSION: This study indicated that school experiences in young schoolchildren may be important determinants of concurrent and later mental health problems.