Background: Several aspects of school life are thought to be associated with increased risk of self-harm in adolescence, but these have rarely been investigated in prospective studies. Methods: Members of the Avon Longitudinal Study of Parents and Children (ALSPAC) birth cohort completed postal surveys of school experiences aged 14, and self-harm behaviour aged 16 (n = 3939). Associations between school experiences (feeling connected to school, enjoyment of school and perception of teachers as fair) and subsequent self-harm were examined using multivariable logistic regression models. Results: Self-harm aged 16 was associated with earlier perceptions of school, specifically not getting on well with or feeling accepted by others (OR = 2.43 [1.76, 3.35] and OR = 2.69 [2.16, 3.35] respectively), not liking school or the work done in class (OR = 1.40 [1.17, 1.69] and OR = 1.36 [1.10, 1.67]), and feeling that teachers are not clear about behaviour or fail to address misbehaviour consistently (OR = 1.59 [1.20, 2.12] OR = 1.89 [1.51, 2.37]). These associations were partially attenuated in models controlling for mental health concurrent with the outcome. Poor school experiences were related to both suicidal and non-suicidal self-harm, with slightly stronger associations visible for the former. Limitations: (i) There was some loss to follow up, (ii) experience of bullying was not measured, and (iii) exposure and outcome measures were self-report. Conclusions: Students who feel unconnected to school, unhappy at school, or feel that teachers are unfair are more likely to self-harm in the future. Assessing students’ perceptions of school may serve to identify those at risk of self-harm who would benefit from preventative interventions.