Chronic inflammation of the flexor hallucis longus (FHL) tendon can result in stenosing tenosynovitis. This condition has been well documented in ballet dancers. It usually presents as posteromedial ankle pain, worsened by plantarflexion activities. Although conservative therapy benefits most patients, some recalcitrant cases may require surgical intervention. This is the first case report that describes the occurrence of this condition in a runner with an anomalous flexor hallucis longus muscle.