A patient with acquired immune deficiency syndrome presented with babesiosis 6 months after presumed tick exposure. Despite initial treatment with azithromycin and atovaquone, followed by quinine and clindamycin, he experienced an increasing parasite load. Finally, red blood cell exchange transfusion, anti-Babesia therapy, and the addition of atovaquone-proguanil to the treatment regimen led to symptomatic improvement and elimination of parasitemia. Low-level parasitemia recurred 20 weeks later and was eradicated by administration of atovaquone-proguanil monotherapy. Atovaquone-proguanil appears to have activity against babesiosis and should be studied as a potential therapy for patients with refractory babesiosis.