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Abstract Background Recent systematic reviews have indicated that cognitive behavioral therapy (CBT) is effective in reducing anxiety symptoms for autistic and non-autistic children. However, the vast majority of CBT research for autistic youth has been implemented within university settings and primarily by mental health providers. Schools hold great promise to equitably manage the mental health symptoms of autistic youth. Although preliminary research evaluating CBT within schools has been promising, CBT has not yet been compared to another readily available school mental health program. The goal of this protocol paper is to describe a multi-site study comparing two school-based interventions, Facing Your Fears-School Based (FYF-SB) and Zones of Regulation (ZOR) via a cluster randomized controlled type 1 hybrid effectiveness-implementation trial to determine which of the two interventions will best support autistic youth with anxiety in schools. Methods Up to 100 elementary and middle schools will be randomized into FYF-SB or ZOR. Once schools are randomized, a minimum of two interdisciplinary school providers at each school will be trained to deliver either FYF-SB or ZOR over the course of 12 weeks to groups of 2–5 autistic students ages 8–14 years. Over the course of two years, a total of 200 autistic students will receive either ZOR or FYF-SB. The primary outcome of this trial is child anxiety, as rated by masked evaluators and via caregiver- and student-report, which will be measured at baseline, post-treatment, and 6-month follow-up. Semi-structured interviews will also be conducted with a purposive sample of students, caregivers, and school providers to understand the acceptability, appropriateness, and feasibility of either ZOR or FYF-SB. Stakeholder engagement is a central component of this project via two stakeholder advisory boards that will directly inform and oversee the project. Discussion Results of this study will provide evidence about the relative impact of two school-based mental health interventions on outcomes reported as meaningful by caregivers and school providers. The additional focus on evaluating factors that support the implementation of FYF-SB and ZOR will allow future studies to test targeted implementation strategies that support mental health programming uptake and implementation within public schools. Trial registration This trial is registered with clinicaltrials.gov (NCT05863520).