Thrombin plays a central role in sepsis pathophysiology. The correlation of thrombin generation (TG) assays with infection severity and prognosis, and whether it can be used as a clinical tool, have been poorly explored and are the subjects of our research. We recruited 130 patients with systemic infection between 2016 and 2019. Patients were divided according to infection severity by using the sequential organ failure assessment (SOFA) and quickSOFA (qSOFA) scores. The hemostatic state was analyzed by Calibrated Automated Thrombogram. The primary end points were TG values and the secondary end point was in-hospital mortality. Patients with qSOFA ≥ 2 had a longer lag time (5.6 vs. 4.6 min) and time to peak (8 vs. 6.9 min) than those with lower scores (p = 0.014 and 0.01, respectively). SOFA ≥ 2 had a longer lag time (5.2 vs. 4.3 min), time to peak (7.5 vs. 6.7 min) and lower endogenous thrombin potential (ETP) (1834 vs. 2015 nM*min), p = 0.008, 0.019, and 0.048, respectively. Patients who died (11) had lower ETP (1648 vs. 1928 nM*min) and peak height (284 vs. 345 nM), p = 0.034 and 0.012, respectively. In conclusion TG assays may be a valuable tool in predicting infection severity and prognosis.