Few technology-based interventions have addressed mathematical and numeracy skills of individuals with autism spectrum disorder (ASD). However, children and adolescents with ASD may experience difficulties in mathematical learning, and even be behind their peers at school. Intelligent Tutoring System (ITS) is an innovative way for enhancing teaching programs through learning optimization algorithms coping interindividual differences in the educational curriculum progress. They have been used with success with typically-developed students for levering on the linkage learning-motivation, but remains at a theoretical stage for students with ASD and/or intellectual disability (ID). We conducted a pilot study to assess an ITS-based intervention embedded into the KidLearn application for instructing mathematical skills (i.e., adding and subtracting numbers between 0 and 100). Twenty-four secondary school students with ASD and/or intellectual disability, enrolled from special education classrooms, have been recruited: 14 students received the KidLearn intervention, while the 10 others received control intervention. Pre-post assessments showed that calculation and motivational measures were significantly improved in KidLearn condition compared to the control condition. ITS intervention appeared relevant for calculation learning in the setting of special education.