Executive functioning (EF) deficits, such as challenges with planning, organization, and materials management, negatively impact academic performance, particularly for middle-school students with autism spectrum disorder (ASD) without intellectual disability (ID). The aim was to assess the initial efficacy of the school-based version of the Achieving Independence and Mastery in School (AIMS) intervention in a pilot randomized clinical trial. 47 autistic middle-schoolers without ID attending nine different schools were randomized to participate in AIMS or to wait to receive AIMS the following semester (waitlist control = WLC). Youth, caregivers, and teachers rated academic EFs and academic functioning, and youth completed an objective EF measure, at baseline and outcome (post). Effect sizes were computed comparing baseline and post measures within each group. Individuals randomized to AIMS improved from baseline to post on academic EF outcome measures with small to moderate effect sizes, compared to WLC, who made some improvements but with generally smaller effect sizes. Analyses with academic functioning measures showed a similar pattern of results. These promising results suggest that AIMS delivered in the school by school-based personnel to small groups of students with ASD without ID can improve academic EF skills.