Clinical and research evidence supports the efficacy of rehabilitative intervention for improving targeted skills or global outcomes in individuals with autism spectrum disorder (ASD). However, putative mechanisms of structural and functional brain changes are poorly understood. This review aims to investigate the research literature on the neural circuit modifications after non-pharmacological intervention. For this purpose, longitudinal studies that used magnetic resonance imaging (MRI)-based techniques at the start and at the end of the trial to evaluate the neural effects of rehabilitative treatment in subjects with ASD were identified. The six included studies involved a limited number of patients in the active group (from 2 to 16), and differed by acquisition method (task-related and resting-state functional MRI) as well as by functional MRI tasks. Overall, the results produced by the selected investigations demonstrated brain plasticity during the treatment interval that results in an activation/functional connectivity more similar to those of subjects with typical development (TD). Repeated MRI evaluation may represent a promising tool for the detection of neural changes in response to treatment in patients with ASD. However, large-scale randomized controlled trials after standardized rehabilitative intervention are required before translating these preliminary results into clinical use. © 2016 Calderoni, Billeci, Narzisi, Brambilla, Retico and Muratori.