It arises from the inferior two-thirds of the posterior surface of the body of the fibula, with the exception of 2.5 cm at its lowest part; from the lower part of the interosseous membrane; from an intermuscular septum between it and the peroneus muscles, laterally, and from the fascia covering the tibialis posterior, medially.

The grooves on the talus and calcaneus, which contain the tendon of the muscle, are converted by tendinous fibers into distinct canals, lined by a mucous sheath.

A diagnostic ultrasound can also be used to diagnose FHL injuries, as it shows the muscle in movement and potential areas of impingement.

[citation needed] After passing through the tarsal tunnel, the flexor hallucis longus tendon must curve around a bony landmark called the sustentaculum tali.

Due to their excessive use of toe flexion, which results in ten times their body weight being applied to this small muscle and tendon, inflammation and irritation is common at the site of the sustentaculum tali.

With this condition, a nodule develops along the FHL tendon which may produce a popping effect during contraction because it drags along surrounding tissues.

If left untreated and continually irritated, stenosis of the tendon may occur, resulting in the big toe becoming stiff and relatively immobile.