INTRODUCTION: Studies have indicated that gait intervention programmes with minimalist shoes are effective for reducing pain, improving functionality and reducing knee joint overload in older women with knee osteoarthritis (OA). Other clinical trials with knee and foot muscle strength training and/or dynamic balance training have also shown clinical and functional effectiveness. Despite promising strategies, there is no evidence of the combination of shoes with gait intervention programmes. Thus, the objective of this randomised clinical trial is to investigate the effects of therapeutic programme of muscular resistance, balance and gait exercises with and without the use of low-cost, flexible shoes on the clinical, functional and biomechanical aspects of older women with medial knee OA. METHODS AND ANALYSIS: This randomised controlled trial with blinded evaluators will involve 36 older women. Twenty-four older women with knee OA (medial compartment) will be randomised to the intervention groups with minimalist shoes (GIC; n=12) or in a barefoot condition (GID; n=12), and 12 older women to the control group (n=12). The intervention protocol will consist of knee-foot muscle resistance and static balance training, reactive and proactive dynamic balance training, and gait training with visual feedback. The intervention will have a duration of two consecutive months, twice a week, totalling 16 sessions. The primary outcomes will be walking pain measured by Visual Analogue Scale and questionnaires: Western Ontario McMaster Universities Osteoarthritis Index and Lequesne Algofunctional. The secondary outcomes will be: 6-min walk test, Falls Risk Awareness Questionnaire, Timed Up and Go Test, and distribution of plantar load during gait and balance by pressure platform. Data will be analysed according to an intention-to-treat approach. ETHICS AND DISSEMINATION: This study involves human participants and was approved by the ethics committee of the Universidade Santo Amaro, School Medicine, São Paulo/SP, Brazil (N°4.091.006). Participants gave informed consent to participate in the study before taking part. Investigators will communicate trial results to participants and healthcare professionals through scientific databases, social media, publications and conferences. TRIAL REGISTRATION NUMBER: RBR-10j4bw25 in Brazilian Clinical Trial Registry.