We report a case of a competitive athlete who complained of chronic pain over the first metatarsal head in the absence of preceding trauma that was exacerbated with forced plantar flexion of the big toe. Initial radiographic findings suggested a tripartite appearance of the medial hallux sesamoid, and the patient was treated as for sesamoiditis. However, persistent symptoms over a period of 12 months necessitated further imaging with magnetic resonance, which confirmed a fracture of the bipartite medial hallux sesamoid. Considering that it is clinically important to differentiate between a tripartite/multipartite hallux sesamoid variant and a fracture of a bipartite hallux sesamoid, an expedient diagnosis is vital to avoiding complications of stress fractures. This can be a diagnostic challenge for the radiologist, emergency physician, and orthopedic surgeon, requiring a high index of suspicion. Accurate and timely diagnosis can be achieved with a clear history, detailed physical examination, and appropriate radiological evaluation.