Malaria, caused by the protozoan Plasmodium is a devastating mosquito-borne disease, that puts nearly half the world’s population at risk1. Despite mounting substantial T and B cell responses, humans fail to efficiently control blood-stage malaria or develop sterilizing immunity to reinfections2. Though Foxp3+ regulatory T cells (Tregs) form a part of these responses3–5, their influence remains disputed, and mode of action unknown. Here we show that Tregs, which expand in both humans and rodents during blood-stage malaria, interfere with conventional T helper (Th) cell responses and the Follicular T helper (Tfh) cell:B cell partnership in germinal centers, in a critical temporal window to impede protective immunity, through the Cytotoxic T-lymphocyte-Associated protein (CTLA)-4. Targeting Tregs or CTLA-4 with precisely timed depletion or blocking enhanced immune responses, accelerated clearance, and generated species-transcending immunity to blood-stage malaria in mice. Our study uncovers a critical mechanism of immunosuppression associated with blood-stage malaria that delays parasite clearance and prevents development of potent adaptive immunity to reinfection. These data also reveal a temporally discrete and therapeutically amenable functional role for Tregs in limiting anti-malarial immunity.