Understanding the molecular mechanisms underlying resistance and tolerance to pathogen infection may present the opportunity to develop novel interventions. Resistance is the absence of clinical disease with low pathogen burden, while tolerance is minimal clinical disease in the face of high pathogen burden. Salmonella is a worldwide health concern. We studied 18 strains of Collaborative Cross mice that survive acute Salmonella Typhimurium (STm) infections. We infected these strains orally and monitored them for three weeks post-infection. Five strains cleared STm by the end of the experiment (resistant), while 6 strains maintained a bacterial load and survived to the end of the experiment (tolerant). The remaining 7 strains survived longer than 7 days but succumbed to infection before the end of the study period and were called “delayed susceptible” to differentiate them from strains that do not survive to day 7 (susceptible). Tolerant strains were colonized in Peyer’s patches, mesenteric lymph node, spleen and liver, while resistant strains had significantly reduced bacterial colonization. Tolerant strains had lower pre-infection core body temperatures than both delayed susceptible and resistant strains and had disrupted circadian patterns of body temperature post-infection sooner than resistant strains. Tolerant strains had higher circulating total white blood cells than resistant strains, driven by increased numbers of neutrophils. Tolerant strains had more severe tissue damage and higher circulating levels of MCP-1 and IFN-γ, but lower levels of ENA-78 than resistant strains. QTL analysis revealed 1 significant association and 6 suggestive associations. RNA-seq analysis identified 22 genes that are differentially regulated in tolerant versus resistant animals that overlapped with the QTLs we identified and allowed us to identify the top 5 canonical pathways. Fibrinogen genes (Fga, Fgb, and Fgg) were found across the QTL, RNA, and top canonical pathways making them the best candidate genes for differentiating tolerance and resistance.