Scrub typhus is the leading source of febrile illness in endemic countries due to infection with Orientia tsutsugamushi (Ot), a seriously understudied intracellular bacterium. Pulmonary complications in patients are common and can develop into life threatening conditions. The diverse antigenicity of Ot genotypes and inter-strain differences seem to be connected to varied virulence and clinical outcomes; however, detailed studies of strain-related pulmonary immune responses in human patients or experimental animals are lacking. In this study, we used two clinically prevalent bacterial strains, Karp and Gilliam, and revealed cellular immune responses in inflamed lungs and potential biomarkers of disease severity. We found that outbred CD-1 mice were highly susceptible to both Karp and Gilliam strains; however, C57BL/6 (B6) mice were susceptible to Karp, but resistant to Gilliam (with self-limiting infection), corresponding to their tissue bacterial burdens and lung pathological changes. Multicolor flow cytometric analyses of perfused B6 mouse lungs revealed robust and sustained influx and activation of innate immune cells (monocytes, macrophages, neutrophils, and NK cells), followed by those of CD4+ and CD8+ T cells, during Karp infection, but such responses were greatly attenuated during Gilliam infection. The robust cellular responses in Karp-infected B6 mice were positively correlated with significantly early and high levels of serum cytokine/chemokine protein levels (CXCL1, CCL2/3/5, and G-CSF), as well as pulmonary gene expression (CXCL1/2, CCL2/3/4, and IFNgamma). In vitro infection of B6 mouse-derived primary macrophages also revealed bacterial strain-dependent immune gene expression profiles. This study provided the first lines of evidence that highlighted differential tissue cellular responses against Karp vs. Gilliam infection, offering a framework for future investigation of Ot strain-related mechanisms of disease pathogenesis vs. infection control.