Atypical B cells are a population of activated B cells that are commonly enriched in individuals with chronic immune activation. Prior studies to determine the function of these cells have yielded conflicting results, possibly due to functional heterogeneity among this B cell population. To better define the role(s) of atypical B cells in the host adaptive immune response, we performed single-cell sequencing of transcriptomes, cell surface markers, and B cell receptors in individuals with chronic Plasmodium falciparum exposure, a condition known to lead to accumulation of circulating atypical B cells. Our studies identified previously uncharacterized populations of atypical B cells with distinct transcriptional and functional profiles: i) anergy or tolerance, ii) increased ability to interact with T cells, and iii) preparation for high translational activity as seen in pre-antibody secreting cells. We identified a set of cell surface markers to distinguish these distinct atypical B cell subsets and confirmed their presence in malaria-experienced children and adults using flow cytometry. P. falciparum-specific cells were present in equal proportions within each of these populations, indicating that all three subsets develop in response to antigen stimulation. Collectively, our findings help explain the conflicting observations in prior studies involving the functions of atypical B cells and indicate the need for reclassification of these cells into multiple distinct subsets to better understand their role in the adaptive immune response in chronic inflammatory conditions.