Intramuscular cysts at the proximal calf are rare; however, their etiology is diverse, making accurate diagnosis and treatment difficult. To our knowledge, there are no previous publications in literature about intramuscular cysts at the proximal calf, arising from different origins. This article describes two rare cases with intramuscular cysts. Case 1 was diagnosed as an intramuscular ganglion cyst arising from the proximal gastrocnemius medialis muscle, and arthroscopic examination as well as open cyst excision was performed. Case 2 was another type, which has never been reported in the literature. It was diagnosed as diffuse pigmented villonodular synovitis (PVNS), with the intramuscular cyst arising from PVNS, and only arthroscopic synovectomy was performed. The diagnoses for these cases were confirmed by histopathology. In addition, we have summarized intramuscular cysts at the proximal calf by a systematic literature review and divided them into five types based on their origin. The five types are, intramuscular cysts arising from the muscular tissue, knee joint, proximal tibiofibular joint, the neurilemma and PVNS. The treatment of intramuscular cysts varies based on their origin; hence, it is important to identify the origin.