BACKGROUND: Multimodal rehabilitation has shown good results in adults with temporomandibular disorder (TMD), but there is still doubt regarding the protocol's ideal format (face-to-face or online), and its effectiveness among adolescents. The purpose of this study is to describe a randomized clinical trial protocol of face-to-face and online multimodal rehabilitation, in adolescents with TMD, and to determine its effects on pain, peripheral oxygenation of the masseter muscle, and mandibular range of motion, kinesiophobia and parafunction. METHODS: A randomized, controlled clinical trial, blinded to statistical analyses, will be carried out, involving 26 adolescents, diagnosed with TMD. After randomization, the participants will be allocated into two groups: (1) telerehabilitation and (2) face-to-face treatment groups. Each group will undergo an initial assessment, followed by three treatment sessions, reassessment, and follow-up. Appointments and reassessments will be face-to-face, with instruments validated and adapted for adolescent age groups. The intervention protocol also aims at practicality, ease of execution, and strategies for the patient to easily self-manage and perform independently, adapted for face-to-face or online formats. The Diagnostic Criteria for Temporomandibular Disorders, physical and psychosocial aspects, algometry, near-infrared spectroscopy, and the Tampa scale for kinesiophobia will be used to assess the outcomes. DISCUSSION: It is expected that this study will contribute to online and face-to-face assessments and demonstrate the differences in the practice of rehabilitation of adolescents with TMD. Data will be published after the study is completed, and if the benefits are proven, care modalities may be implemented. TRIAL REGISTRATION: REBEC-RBR-5scd5tm, UTN code: U1111-1288-4495 . Registered on 19 May 2023.