The school inclusion of students with autism is still a challenge. To address the cognitive underpinnings of school-related adaptive behaviors, 27 students with autism and 18 students with intellectual and/or severe learning disability, aged from 11 to 17, were recruited. They underwent socio-emotional processing and executive functioning assessments, as well as school-related adaptive behavior and quality of life measurements. Both groups performed equally on socio-emotional and executive assessments, and they reported the same low quality of life. However, students with autism exhibited more limitations than the students with intellectual disabilities on complex school adaptive behaviors (socialization and autonomy) and problem behaviors, but both groups performed equally on more basic adaptive behaviors (school routines, communication). Multiple regression analyses highlighted between-group differences in terms of adaptive functioning profiles, which were linked with different cognitive predictors according to students' medical conditions. The greater school-related limitations of students with autism were mostly explained by socio-emotional performance, while IQ (intellectual quotient) mostly explained the comparable between-group limitations. The low quality of life of both groups was slightly explained by executive performance. The role of both socio-emotional and executive functioning in students' adaptive behaviors and quality of life suggests remediation targets for promoting the school inclusion of students with autism.