Students who report high levels of intrinsic motivation (IM) perform better on academic tasks compared with students who report low levels of IM. However, there is a paucity of data on IM for several disability categories (e.g., intellectual disability). The focus of this study was to use a nationally representative sample of students with disabilities to understand whether teachers’ perceptions of students’ academic IM varied by disability categories. Correlation and regression models were used to determine factors that influenced teachers’ perceptions of academic IM for students with disabilities. Controlling for external factors, such as parental expectation of their child’s academic career and teachers’ pedagogical competence, attenuated gaps in teacher perception of student IM between students with intellectual disability and learning disability. Including student classroom collaboration variables such as frequency of participation in peer work and classroom discussion to the model reduced disparities in teacher-perceived academic IM between students with autism and learning disabilities.