Since the initial reported outbreak of coronavirus disease 2019 (COVID-19), many unique case reports have been published in the medical literature. Here we report a complicated clinical course of a young patient with COVID-19 who presented initially with recurrent autoimmune hemolytic anemia (AIHA). He subsequently developed bilateral pulmonary emboli, and ultimately succumbed to encephalitis and cryptococcemia in the context of being treated with high dose immunosuppression for the AIHA. Combining immunosuppression with active COVID-19 infection presents some truly challenging diagnostic and management scenarios which this case summarizes and highlights very well. Based on this case, we propose some strategies on how to approach these difficult decisions while also recognizing the significant gaps that exist in such an evolving topic. Lastly, this case also represents a potentially novel presentation of secondary fungal infection of the central nervous system (CNS) related to COVID-19.