The current study used developmental trajectories to examine the relationship between internalising and externalising behaviours and victimisation over the transition period from primary to secondary school. Data were collected using a self-completion questionnaire four times over 3 years from 3,459 students aged 11-14 years. Students were tracked longitudinally to assess their knowledge, attitudes, mental health and bullying experiences during the transition period. Multilevel modelling was used to examine the relationship between developmental victimisation trajectories and behavioural and emotional difficulties over time of students’ transitioning from primary to secondary school. Males who experienced low, but increasing, levels of victimisation over secondary school had greater emotional symptoms, conduct problems, hyperactivity, peer problems and lower pro-social behaviour than those who had not been victimised. Whereas females who experienced low, but increasing, levels of victimisation over secondary school had greater emotional symptoms and peer problems than those who had not been victimised. The current results highlight the need to prevent the continuation or escalation of chronic victimisation from primary to secondary school and to improve the emotional wellbeing of adolescents. It is recommended that whole-school bullying prevention and intervention programs and social wellbeing programs are implemented during primary school and the transition to secondary school.