Abstract Background The school is a key setting for the provision of mental health services to children, particularly those underserved through traditional service delivery systems. School-wide Positive Behavioral Interventions and Supports (PBIS) is a tiered approach to service delivery based on the public health model that schools use to implement universal (Tier 1) supports to improve school climate and safety. As our prior research has demonstrated, PBIS is a useful vehicle for implementing mental and behavioral health evidence-based practices (EBPs) at Tier 2 for children with, or at risk for, mental health disorders. Very little research has been conducted regarding the use of mental health EBPs at Tier 2 or how to sustain implementation in schools. Methods/design The main aim of the study is to compare fidelity, penetration, cost-effectiveness, and student outcomes of Tier 2 mental health interventions across 2 sustainment approaches for school implementers in 12 K-8 schools. The study uses a 2-arm, cluster randomized controlled trial design. The two arms are: (a) Preparing for Sustainment (PS)—a consultation strategy implemented by school district coaches who receive support from external consultants, and (b) Sustainment as Usual (SAU)—a consultation strategy implemented by school district coaches alone. Participants will be 60 implementers and 360 students at risk for externalizing and anxiety disorders. The interventions implemented by school personnel are: Coping Power Program (CPP) for externalizing disorders, CBT for Anxiety Treatment in Schools (CATS) for anxiety disorders, and Check-in/Check-out (CICO) for externalizing and internalizing disorders. The Interactive Systems Framework (ISF) for Dissemination and Implementation guides the training and support procedures for implementers. Discussion We expect that this study will result in a feasible, effective, and cost-effective strategy for sustaining mental health EBPs that is embedded within a multi-tiered system of support. Results from this study conducted in a large urban school district would likely generalize to other large, urban districts and have an impact on population-level child mental health. Trial registration ClinicalTrials.gov identifier number NCT04869657. Registered May 3, 2021.