Background: Despite improvements in antimicrobial therapy and supportive care, sepsis is still a major public health issue. Recently, CD100 and its receptor in the immune system CD72 were shown to play a major role in immune regulation. The purpose of this study was to investigate the expression and clinical correlations of CD72 and CD100 on circulating lymphocytes of septic patients. Methods: In total, 24 healthy controls and 54 septic patients were enrolled in this study. Considering the focus of the current study was on the immunosuppressive phase of sepsis, blood samples of patients were collected at days 3-4 after the onset of sepsis. The levels of CD72 and CD100 expression on circulating lymphocytes were measured by flow cytometry and serum IL-6, IL-10, and immunoglobulin M levels were determined by enzyme-linked immunosorbent assay. Results: Our results showed that the levels of CD100 expression on T cells and CD72 expression on B cells were significantly lower in septic patients. Similarly, a significant decrease in the expression levels of CD72 and CD100 was observed in non-survivors compared with survivors. In addition, the reduction of immunoglobulin M levels and lymphocyte counts were correlated with the low CD72 and CD100 expression levels. Multivariate logistic regression analysis showed that the percentage of CD100(+)/CD8(+)T cells and CD72(+)/CD19(+)B cells were independent predictors of 28-day mortality in septic patients. Simultaneously, the receiver operating characteristic curve analysis showed that the combination of the percentage of CD100(+)/CD8(+)T cells and sequential organ failure assessment score had the best predictive value of mortality risk. Conclusions: Our study demonstrated that the decrease of the levels of CD72 and CD100 expression on circulating lymphocytes after 3-4 days of sepsis had a close correlation of the 28-day mortality of septic patients. Thus, CD72 and CD100 are promising biomarkers for assessing the prognosis of patients with sepsis. Trial registration: Peripheral blood lymphocytes analysis detects CD72 and CD100 alteration in trauma patients; ChiCTR1900026367; Registered 4 October 2019; http://www.chictr.org.cn.