The aim of this study was to evaluate the occurrence of anatomical variations of the musculotendinous junction of the flexor hallucis longus muscle. Eighty cadaver specimens preserved according to Thiels method were assessed. Following careful dissection, the distance between the musculotendinous junction and the bone–cartilage border of the distal tibia was determined. Three typical anatomical variations were found: (1) a long lateral and shorter medial muscle belly; (2) equal-length medial and lateral muscle bellies; (3) a long medial and shorter lateral muscle belly. As a special variation in two cases only one lateral muscle belly was found. When planning a flexor hallucis longus transfer, preoperative magnetic resonance tomography (MRT) should be carried out in order to guarantee sufficient coverage of an existing soft tissue defect. These anatomical characteristics have also to be considered when interpreting ultrasonic or MRT findings in this region.