Although mental health problems are common in autism, relatively little is known about their stability and the factors that influence their persistence or change over the life-course. To address this, we use data from the Special Needs and Autism Project (SNAP) cohort studied at three time-points from 12 to 23 years. Using the parent-reported Strengths and Difficulties Questionnaire (SDQ) domains of conduct, emotional, and ADHD symptoms, we evaluated the role of child, family, and contextual characteristics on these three trajectories. Symptoms decreased significantly over time for all three domains, but many participants still scored above the published disorder cutoffs. Individuals showed high levels of persistence. Higher initial adaptive function and language levels predicted a greater decline in conduct and ADHD symptoms. In contrast, higher language functioning was associated with higher levels of emotional symptoms, as was lower levels of autism symptom severity and higher parental education. Those with higher neighborhood deprivation had higher initial conduct problems but a steeper decline over time. Our findings highlight that it may be possible to accurately predict mental health trajectories over this time period, which could help parents and carers in planning and help professionals target resources more efficiently.