This study investigated the differences between the mathematical profiles of primary school pupils with intellectual disabilities (ID) enrolled in inclusive classrooms and those enrolled in special schools. It also considered whether the instructional setting has an impact on mathematical achievement gain. The mathematical achievement of 100 pupils with ID in inclusive classrooms (groupINCLUSIVE, n = 44) and special schools (groupSPECIAL, n = 56) was assessed at the beginning and the end of one school year. The results show that pupils with ID have a different mathematical profile in each setting. More of the pupils with very low mathematical achievement were enrolled in special schools and they made little progress over the course of the year. More of the pupils with ID who had computational skills were in inclusive classrooms. Due to large differences in age, IQ, and prior mathematical achievement between the two groups, a sample of matched pairs with one pupil from each setting was selected (n = 44). Regression analysis showed that the inclusive setting had a small positive effect on mathematical achievement gain after nine months. The study provides evidence that inclusive education is beneficial for the mathematical achievement gain of pupils with ID.