Malaria-specific antibody responses are short lived in children, leaving them susceptible to repeated bouts of febrile malaria. The cellular and molecular mechanisms underlying this apparent immune deficiency are poorly understood. Recently, T follicular helper (Tfh) cells have been shown to play a critical role in generating long-lived antibody responses. We show that Malian children have resting PD-1+CXCR5+CD4+ Tfh cells in circulation that resemble germinal center Tfh cells phenotypically and functionally. Within this population, PD-1+CXCR5+CXCR3− Tfh cells are superior to Th1-polarized PD-1+CXCR5+CXCR3+ Tfh cells in helping B cells. Longitudinally, we observed that malaria drives Th1 cytokine responses, and accordingly, the less-functional Th1-polarized Tfh subset was preferentially activated and its activation did not correlate with antibody responses. These data provide insights into the Tfh cell biology underlying suboptimal antibody responses to malaria in children and suggest that vaccine strategies that promote CXCR3− Tfh cell responses may improve malaria vaccine efficacy. Display omitted •Circulating PD-1+CXCR5+CD4+ T cells in malaria-exposed children resemble GC Tfh cells•The CXCR3− Tfh subset is superior to the Th1-like CXCR3+ subset in helping B cells•Malaria induces Th1 cytokines and activates the less-functional CXCR3+ Tfh subset•Tfh cell responses to malaria do not correlate with B cell and antibody responses Malaria-specific antibody responses are short lived in children, leaving them susceptible to repeated malaria infections. Tfh cells are critical for long-lived antibody responses. Obeng-Adjei et al. provide evidence that malaria activates less-functional Th1-like PD-1+CXCR5+CXCR3+ Tfh cells that are disassociated from B cell/antibody responses.