School absenteeism is a significant social and public health problem, and it has considerable negative consequences on the development of children and adolescents not only in the short term but also in the long term. We investigated special education needs (SEN) as a risk factor for absenteeism. For 418,455 mainstream secondary school students from 151 local authorities in England, multilevel linear regression models were run to investigate the association between SEN, SEN types and absenteeism during their secondary school period from year 7 to year 11. Local authority level variation was also investigated. Adolescents with SEN were more likely to be absent than their peers without SEN. Of adolescents with SEN, those with physical disability, followed by those with behavioural, emotional and social difficulties had the highest rates of absenteeism. Absenteeism rates increased as adolescents grew older. The association between absenteeism and having any SEN varied substantially across Local authorities. The results suggest that early interventions/preventative measures could mitigate loss of schooling due to absence. Moreover, the substantial variation in attendance for children across different local authorities suggest that there may be scope for local authorities to influence absence rates among adolescents.