Introduction: Dengue and Chikungunya arboviral diseases are considered major public health challenges in tropical regions due to high infection rates and the occurrence of musculoskeletal sequelae that impair strength, balance, and functionality. After the acute phase, symptoms such as fatigue, joint pain, muscle weakness, and postural instability are common, reducing quality of life and hindering social and occupational reintegration.Objective: To analyze the effects of a rehabilitation protocol on muscle fatigue, muscle strength, and postural control in post-Dengue and Chikungunya patients.Methods: This is a non-randomized clinical trial conducted at the Integrated Laboratory for Research and Care in Infectious and Sequelae Diseases (LabDIS/UEPA). Individuals of both sexes, aged over 18 years, with a confirmed diagnosis of Dengue and/or Chikungunya within the last five years will be included. Data collection will include a clinical interview, surface electromyography of the flexor carpi radialis, tibialis anterior, lateral and medial gastrocnemius muscles, hydraulic and electronic dynamometry, manovacuometry, and baropodometry. The rehabilitation protocol will consist of twenty supervised sessions of aerobic, anaerobic, and respiratory exercises.Expected Results: Improvements in muscle strength, muscle fatigue, and postural control are expected following the intervention.Conclusion: The findings may support physiotherapeutic strategies aimed at improving strength, fatigue, and balance, expanding knowledge on the neuromuscular and respiratory consequences of arboviral diseases, and contributing to the development of evidence-based rehabilitation protocols, with potential positive impacts on healthcare delivery and public health policies.