Recent research has shown that autistic children are reported to have lower school attendance than non-autistic students. School non-attendance can occur for multiple reasons, including attendance at medical/health appointments and school refusal/emotionally based school avoidance. Providing support to improve autistic children’s school attendance requires an understanding of the factors that potentially lead to or influence specific types of school non-attendance. The aim of this study was to identify concurrent and longitudinal school, family, and child factors associated with school non-attendance in autistic children. Parents/caregivers who had previously participated in a 6 year longitudinal study in Australia were invited to complete a follow-up online survey about their child’s school attendance. Seventy-seven parents of autistic children aged 11–14 years participated. Over 40% of children had persistent absence (> 10% days) from school. Based on multivariate negative binomial regression models, child anxiety was a significant predictor of days missed for multiple types of school non-attendance. Other factors, including child sensory processing differences, child behavioural and emotional challenges, parent stress, family income, and parent employment, were correlated with specific absence types. Child anxiety was the strongest and most consistent longitudinal predictor, with higher child anxiety significantly predicting more days of school non-attendance 3, 4, and 6 years later. Findings highlight the importance of considering school, child, and family factors specific to different types of school non-attendance to support autistic children. Identifying factors that lead to child anxiety and preventing/reducing child anxiety early is a potentially promising avenue to support attendance.