Fungal prosthetic joint infection (fPJI) is a rare complication; nonetheless, it represents a significant diagnostic and therapeutic challenge. There are no official guidelines on the most effective approach to identify and treat fPJIs. This systematic review aims to review the current literature on fPJI management and provide a comprehensive overview of this topic, especially from an epidemiologic point of view. Studies eligible for this systematic review were identified through an electronic systematic search of PubMed, Scopus, and Web of Science until 30 September 2022. Further references were obtained by cross-referencing. Sixty-three studies met the inclusion criteria, reporting on 372 cases of fPJI; such cases were described mostly in case reports and small case series with only a few larger cohort studies. Diagnosis of fPJI is challenging because of its chronic and indolent clinical course; it is further complicated by the technical difficulty of harvesting fungal cultures. A two-stage revision was the primary procedure in 239 (64.2%) patients whereas DAIR and one-stage approaches were reported in 30 (8.0%) and 18 (4.8 %) cases. In conclusion, our study highlights the heterogeneity of the reported treatments of fPJI, particularly in terms of medical management. With concern to a surgical approach, a two-stage revision arthroplasty is generally suggested, considering fPJI a delayed or late infection. The need for multicenter, prospective studies to provide standardized protocols and improve the treatment of fungal PJI clearly emerges.