Many children with disabilities engage in less physical activity compared to their peers. This pilot-feasibility study examines the effects of movement-based desk and alternative seating on classroom physical activity, time on task, reading fluency, and reading comprehension scores in fourth/fifth and seventh/eighth-grade children with disabilities. Using a cross-over 8-week design, action desks were included in fourth/fifth (N = 14) and seventh/eighth (N = 21) grade classrooms for students with disabilities. Levels of physical activity were measured using accelerometers; reading ability was assessed using AIMSweb Oral Reading Fluency and MAZE probes; time on task was measured using video recordings over 3 consecutive days. Data were collected at 0-week, 4-week, 8-week, 12-week, and 16-week time points. A significant increase in metabolic equivalent was seen in fourth/fifth graders and a significant decline in time spent in sedentary activity were observed in both fourth/fifth and seventh/eighth graders. The fourth/fifth graders increased their time spent in moderate physical activity and time on task during the intervention whereas seventh/eighth graders improved oral reading fluency. How a physical activity-based classroom may be an effective intervention in students with disabilities to improve levels of physical activity and improve academic learning is discussed.