Patients with septic acute kidney injury (AKI) often require continuous renal replacement therapy (CRRT) , but factors that predict their prognosis have been insufficiently established. Thus, this study aimed to evaluate the associations of the Sequential Organ Failure Assessment (SOFA) score, SOFA-sub scores, and SOFA sub-score components with mortality in patients with AKI on CRRT. A total of 231 patients with AKI who required CRRT were enrolled in this retrospective, cohort study. Associations between the SOFA-sub scores on days 1 or 4 of CRRT and all-cause death within 30 days were assessed. The respiratory SOFA subscore in patients with sepsis on day 1 was associated with mortality. However, this association disappeared on day 4, and coagulation and renal SOFA-sub scores were significantly associated with mortality in patients with sepsis. These findings differed from patients without septic AKI.The baseline respiratory SOFA sub-score was significantly associated with mortality in patients with septic AKI, whereas the coagulation SOFA sub-score became a prognostic factor on day 4. The evaluation of SOFA-sub scores and changes in the factors after CRRT initiation may be useful for predicting prognosis in patients with septic AKI.