Although there are numerous reports of septic pyogenic arthritis after arthroscopic anterior cruciate ligament (ACL) reconstruction, there is limited information regarding the outcomes of fungal infection. We determined the outcomes of six patients with mycotic infection after regular ACL reconstruction. There were four males and two females with a mean age of 33 years. We determined the number of procedures performed, bone loss originating to control infection, and final reconstruction in these patients. An average of five arthroscopic lavage procedures had been performed at the referring centers. Fungal infection was diagnosed based on pathologic samples; five infections were the result of mucormycosis and one was Candida. After final débridement, the mean segmental bone loss was 12.8 cm. All patients were treated with intravenous antifungal coverage and cement spacers before final reconstruction. At final followup, all patients were free of clinical infection. Three had reconstruction with an allograft-prosthesis composite, two with hemicylindrical allografts, and one with an intercalary allograft arthrodesis. Despite the extremely unusual presentation of this complication, surgeons should be aware of potential and catastrophic consequences of this severe complication after ACL reconstruction.