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Femoral shaft stress fractures in athletes are not common but pose a great diagnostic challenge to clinicians. Because of few clinical signs, diagnosis and treatment are often delayed. Furthermore, if not treated correctly, these fractures are well known for complications and difficulties.To develop a well structured and reproducible treatment algorithm for athletes with femoral shaft stress fractures.The proposed algorithm is carried out in four phases, each lasting three weeks, and the move to the next phase is based on the result of the tests carried out at the end of the previous phase. Over nine years, we treated seven top level athletes, aged 17–21. In all athletes, diagnosis was based on physical examination, plain radiographs, and bone scan.As a result of the treatment method, all the athletes were fully engaged in athletic activity 12–18 weeks after the beginning of treatment. After completion of the treatment, the athletes were followed up for 48–96 months. During the follow up, there was no recurrence of discomfort or pain, and all the athletes eventually returned to competition level.These results and data available from the literature suggest that the algorithm is the optimal treatment protocol for femoral shaft stress fractures in athletes, avoiding the common complications and difficulties.