Health-related behaviours (HRBs) have been considered one of the most critical public health issues, especially for those with special educational needs (SEN). Previous research suggests that health-related behaviours are highly likely to impact well-being and academic achievement. Diet is a crucial health-related behaviour that needs to be investigated along with factors such as sleep and exercise. The present study used data from the Cornish Academies Project, and secondary analyses were conducted to investigate associations between health-related behaviour and well-being and academic performance of secondary students with SEN. The current study sample was 308 students with SEN (mean age, 13.5 years, SD 1.44 years). The study was longitudinal, with time points 6 months apart, and a multivariate design with data from three academies in Cornwall, United Kingdom. The Diet and Behaviour Scale (DABS) measured diet and lifestyle (physical activity, sleep, and general health). Logistic regressions on the time one data showed a significant relationship between good general health and long sleep, eating healthy foods, and avoiding junk food. High exercise and high attendance decreased the likelihood of low attainment. Long sleep was associated with better conduct at time one and time two. There was a significant association between high consumption of healthy foods and good general health and better educational attainment at time two. Longitudinal cross-lagged analyses showed that high tea and high total weekly caffeine consumption at time one were associated with anxiety at time two. In addition, high cola consumption at time one was associated with high depression at time two. Findings from the current study increase our knowledge regarding associations between HRB and well-being, and academic performance in secondary school pupils with SEN, though the results need to be explored further to determine the precise nature of the relationship.