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.