Autism Spectrum Disorder is a neurodevelopmental disorder characterized by deficits in social communication and interaction as well as the presence of repetitive, restricted patterns of behavior, interests, or activities. Many autistic students experience difficulty with daily functioning at school and home. Given these difficulties, regular school attendance is a primary source for autistic students to receive an appropriate range of needed educational and therapeutic interventions. Moreover, school absenteeism (SA) is associated with negative consequences such as school drop-out. Therefore, early SA prediction would help school districts to intervene properly to ameliorate this issue. Due to its heterogeneity, autistic students show within-group differences concerning their SA. A comprehensive statistical analysis performed by the authors shows that the individual and demographic characteristics of the targeted population are not predictive factors of SA. So, we used the students’ recent previous attendance to predict their future attendance. We introduce a deep learning-based framework for predicting short-and long-term SA of autistic students using the Long Short-Term Memory (LSTM) and Multilayer Perceptron (MLP) algorithms. The adopted algorithms outperform other machine learning algorithms. In detail, LSTM increased the accuracy and recall of short-term SA prediction by 20% and 13%, while the same scores of long-term SA prediction increased by 5% using MLP.