Patients with chronic kidney disease (CKD) often have impaired immune function, making them more prone to infections that can lead to sepsis. The coexistence of these conditions can result in decreased hemoglobin levels and is associated with a higher mortality rate. To investigate whether the transfusion of red blood cells (RBCs) improves the prognosis of septic patients with concomitant CKD and to explore the indications for red blood cell transfusion. This retrospective cohort study utilizes data from the MIMIC-IV (v2.0) database. The study enrolled 6,604 patients with sepsis and concomitant CKD admitted to the Intensive Care Unit (ICU). Propensity score matching (PSM) was applied to adjust for confounding factors. Multivariate Cox regression analysis revealed an association between RBC transfusion and a decreased risk of 28-day mortality (HR: 0.61, 95% CI: 0.54–0.70, P < 0.001). Following a meticulous 1:1 propensity score matching analysis between the two cohorts, the matched population revealed a notable decrease in 28-day mortality within the RBC transfusion group (HR: 0.60, 95% CI: 0.51–0.71; P < 0.001). Additionally, we observed that a SOFA score ≥ 5, a Base Excess (BE) value < 3, and an estimated Glomerular Filtration Rate (eGFR) < 30 may be considered when evaluating the potential need for RBC transfusion. This study demonstrated an association between RBC transfusion and decreased 28-day mortality in patients with sepsis accompanied by CKD. The patient’s BE value, SOFA score, and eGFR are crucial factors influencing the treatment outcome and should be considered when deciding on RBC transfusion.