Purpose: The aim of this study is to compare the effects of Core Foot System muscle training vs. traditional rehabilitation methods in female patients after a hallux valgus correction surgery. Methods: The project will involve 60 women who have undergone a Scarf osteotomy to correct the deformity. Participants will be divided into a control and experimental group. The experimental group will follow the Core Foot System protocol, whereas the control group will perform standard lower-limb exercises. Outcome measures will be collected twice: before the intervention and after eight weeks. Gait will be assessed using the Zebris FDM-2 platform, measuring ground reaction forces during walking. Results: The effects of the exercises on the cross-sectional area of the abductor hallucis muscle and the flexor digitorum brevis muscle will be measured. Foot architecture and arch height will be measured using a podoscope. In addition, the participants will complete the Short Form Health Survey and the American Orthopaedic Foot and Ankle Society questionnaires. Conclusions: The study is expected to provide evidence of the effectiveness of foot muscle training using the protocol. The findings may lead to an improved protocol of rehabilitation in patients after a correction surgery that may result in improved gait parameters and quality of daily life. In the future, an improved therapeutic method should make it possible to boost the effectiveness of physiotherapy in patients after a corrective surgery in the forefoot area. The study has been registered with clinicaltrials.org (NCT05210127; 13 January 2022).