Toll-Like Receptor (TLR) 9 stimulation is required for induction of potent immune responses against pathogen invasion. The use of unmethylated CpG as adjuvants in vaccines provides an excellent means of stimulating adaptive immunity. Our data demonstrate that CpG-C provided prolonged immune responses in the mouse model of tuberculosis when formulated with liposomes and the Mycobacterium tuberculosis antigen ESAT-6. A reduction in the mycobacterial burden was best achieved when administered as an intranasal vaccine and was dependent on type I interferon (IFN). There was a significant difference between CpG-C inoculated wild type and IFN-αR1^−/− mice, indicating that type I IFN plays a role in the immune response following CpG-C inoculation. Further analysis showed that early NK cell presence was not an absolute requirement, although elevated IFN-γ levels were detected in the lungs of mice within 48 h. The reduction in mycobacterial burden was MyD88-independent as CpG-C inoculated MyD88^−/− mice showed comparable mycobacterial burdens to wild type mice with no detriment due to the lack of MyD88. Together our data show that pulmonary stimulation of TLR9 bearing antigen presenting cells resulted in the induction of protective immunity against M. tuberculosis infection that was dependent on type I IFN signaling.