There is limited literature comparing the clinical parameters and treatment outcomes in HIV-infected and HIV-uninfected myasthenia gravis (MG) patients. The aim of the study was to investigate the clinical differences and treatment outcomes in the two categories of patients, particularly the safe use of immunosuppressive therapy in immunocompromised patients. The study was a retrospective analysis of medical records of MG patients from the neuromuscular unit at Inkosi Albert Luthuli Central Hospital in Kwa-Zulu Natal between 2003 and 2019. One hundred and seventy-eight (178) patients fulfilled the clinical criteria for MG. Twenty-four (13.4%) were HIV-infected and 154 (86.5%) were HIV-uninfected. There were 116 (65%) females, median 45 years, (IQR 40–62), 90 (50.5%) black African, 66 (37%) Indian, 20 (11.2%) white, and 2 (1.1%) of mixed ancestry. In the HIV-infected cohort, 20 (87%) had generalized MG, 12 (50%) bulbar, and 14 (60.9%) respiratory onset MG, 12 (50%) presented with MG Foundation of America (MGFA) class five diseases at diagnosis, six (25%) presented with MG crisis during the 5-year follow-up. Thirteen (54%) of the HIV-infected group required rescue therapy using (plasma exchange or IV immunoglobulin) combined with pulse cyclophosphamide compared with 17 (11%) in the HIV-uninfected cohort, respectively. At 5 years, 8 (33%) of the HIV-infected group remained refractory to treatment compared with 10 (6.5%) HIV-uninfected cohort, respectively. No adverse events were documented in HIV-infected patients receiving combination rescue therapy (PLEX or IVIG combined with IV cyclophosphamide). In conclusion HIV-infected MG patients are more likely to require combination rescue therapy with PE/IVIG and IV cyclophosphamide compared with those who were HIV-uninfected. No side effects were documented in the HIV-infected group receiving the above therapy.