Administration of the bacterial protein flagellin to mice activates innate immune signaling that protects against an array of challenges, including ionizing radiation. Herein, we define the underlying mechanism for this protection. We report that flagellin treatment induces proliferation and mobilization of bone marrow cells that aid survival following irradiation. Specifically, treatment of mice or bone marrow cells ex vivo with flagellin induced Toll-like receptor 5 (TLR5)-dependent and NOD-like receptor C4-independent proliferation of Lin-Sca-1+Kit+ (LSK) cells, which includes both hematopoietic stem cells that provide long-term repopulation (LTR) and multipotent progenitor cells (MPPs) that transiently proliferate and differentiate into a range of blood cell types. TLR5 expression on bone marrow cells was necessary and sufficient for flagellin-induced LSK proliferation. Flagellin treatment stimulated LSK proliferation by inducing a 10-fold increase in type 3 MPP (MPP3) without a concomitant increase in LTR cells. Cotransfer of 5 × 103 fluorescence-activated cell sorted flagellin-induced MPP3 cells along with 1 × 105 whole bone marrow cells to lethally irradiated mice revealed that such cells predominantly repopulated the neutrophil compartment for up to 4 week, and dramatically increased the survival rate of the bone marrow transplantation procedure. Hence, we propose the administration of MPP3 cells, elicited by flagellin, as a novel approach to prevent life-threatening neutropenia that can accompany bone marrow transplant and other myeloablative therapeutic procedures.