Effective resolution of malaria infection by avoiding pathogenesis requires regulated pro- to anti-inflammatory responses and the development of protective immunity. TLRs are known to be critical for initiating innate immune responses, but their roles in the regulation of immune responses and development of protective immunity to malaria remain poorly understood. In this study, using WT, TLR2−/−, TLR4−/−, TLR9−/−, and MyD88−/− mice infected with P. yoelii, we show that TLR9 and MyD88 regulate pro-/anti-inflammatory cytokines, Th1/Th2 development, and cellular and humoral responses. DCs from TLR9−/− and MyD88−/− mice produced significantly lower levels of pro-inflammatory cytokines and higher levels of anti-inflammatory cytokines than DCs from WT mice. NK and CD8+ T cells from TLR9−/− and MyD88−/− mice showed markedly impaired cytotoxic activity. Further, mice deficient in TLR9 and MyD88 showed higher Th2 type and lower Th1 type IgGs. Consequently, TLR9−/− and MyD88−/− mice exhibited compromised ability to control parasitemia and were susceptible to death. Our data also show that TLR9 and MyD88 distinctively regulate immune responses to malaria infection. TLR9−/− but not MyD88−/− mice produced significant levels of both pro- and anti-inflammatory cytokines, including IL-1β and IL-18, by other TLRs/inflammasome- and/or IL-1R/IL-18R-mediated signaling. Thus, while MyD88−/− mice completely lacked cell-mediated immunity, TLR9−/− mice showed low levels of cell-mediated immunity and were slightly more resistant to malaria infection than MyD88−/− mice. Overall, our findings demonstrate that TLR9 and MyD88 play central roles in the immune regulation and development of protective immunity to malaria, and have implications in understanding immune responses to other pathogens.