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Background: Fungal prosthetic joint infections (PJIs) are rare, especially those caused by non-<i>Candida</i> species. Treatment has not been fully elucidated, since a plethora of antifungal and surgical interventions have been proposed. Τhis study represents an effort to clarify the optimal management of non-<i>Candida</i> fungal PJIs, by reviewing all relevant published cases. Methods: A thorough review of all existing non-<i>Candida</i> fungal PJIs in the literature was conducted. Data regarding demographics, responsible organisms, antifungal treatment (AFT), surgical intervention, time between initial arthroplasty and onset of symptoms, and time between onset of symptoms and firm diagnosis, as well as the infection’s outcome, were evaluated. Results: Forty-two PJIs, in patients with mean age of 66.2 years, were found and reviewed. <i>Aspergillus</i> spp. were isolated in most cases (10; 23.8%), followed by <i>Coccidioides</i> spp. (7; 16.7%) and <i>Pichia</i><i>anomala</i> (5; 11.9%). Fluconazole was the preferred antifungal regimen (20 cases; 47.6%), followed by amphotericin B (18 cases; 42.9%), while the mean AFT duration was 9.4 months (SD = 7.06). Two-stage revision arthroplasty (TSRA) was performed in 22 cases (52.4%), with the mean time between stages being 5.2 months (SD = 2.9). The mean time between initial joint implantation and onset of symptoms was 42.1 months (SD = 50.7), while the mean time between onset of symptoms and diagnosis was 5.8 months (SD = 14.3). Conclusions: Non-<i>Candida</i> fungal PJIs pose a clinical challenge, demanding a multidisciplinary approach. The present review has shown that combination of TSRA separated by a 3–6-month interval and prolonged AFT has been the standard of care in the studied cases.