Streptococcus pneumoniae is the leading cause of community-acquired pneumonia. Mertk is a receptor tyrosine kinase and a member of the TAM family. It serves as an efferocytosis receptor involved in the recognition and removal of apoptotic debris by phagocytic cells, dampening the inflammatory response. Here we show that at 24h post-inoculation with S. pneumoniae, Mertk-/- mice generated through homologous recombination and backcrossed (HRB-Mertk-/- mice) have fewer bacteria present in their pneumonic lung than wild type mice. This enhanced clearance was not observed in Mertk-/- mice generated by CRISPR technology. The enhanced clearance of HRB-Mertk-/- mice was associated with fewer neutrophils and more IFNγ in the bronchoalveolar lavage, but was not prevented by a neutralizing IFNγ antibody. Mertk is highly expressed on alveolar macrophages. Transcriptomic changes observed in HRB-Mertk-/- alveolar macrophages were associated with leukocyte activation, cellular motility, and response to stimulus, suggesting that they are primed for an inflammatory response. HRB-Mertk-/- mice similarly had enhanced host defense pathways in S. pneumoniae-stimulated alveolar macrophages in vitro and in pneumonic lung tissue. However, HRB-Mertk-/- alveolar macrophages demonstrated no defect in phagocytosis and acidification in vivo, and genes and gene sets describing phagocytic pathways were not enriched, suggesting that the enhanced clearance may be through alterations in the lung microenvironment. HRB-Mertk-/- mice are reported to have a long 129P2 DNA insert (~645 genes) in chromosome 2 adjacent to Mertk, as well as other alterations at multiple sites. Thus, while Mertk deficiency may contribute to the enhanced bacterial clearance, it is not solely responsible, because the phenotype is not seen in the CRISPR-Mertk-/- mice. The 129P2 DNA insert in the HRB-Mertk-/- mice must be mediating at least some of this phenotype. Understanding the mechanistic differences and the means by which this 129P2 DNA insert enhances bacterial clearance remains critically important.