Disseminated Acanthamoeba species infection is likely an underrecognized and underdiagnosed opportunistic infection in patients with advanced human immunodeficiency virus (HIV) disease in South Africa. It presents a unique clinical challenge in that the diagnosis can be difficult to establish and management options are limited in low-resource settings. To our knowledge, there is a paucity of literature to date on the successful use of combination treatment options for patients in low-resource settings without access to miltefosine. We present a case describing the clinical improvement of disseminated Acanthamoeba infection in a patient with advanced HIV using a non-miltefosine-based treatment regimen. The case serves to highlight that Acanthamoeba sp. infection should be considered as a differential diagnosis for nodular and ulcerative cutaneous lesions in patients with advanced HIV in South Africa, and that although there are alternative options for combination treatment in countries without access to miltefosine, efforts should be made to advocate for better access to miltefosine for the treatment of acanthamoebiasis in South Africa.