Background: The sequential organ failure assessment (SOFA) score has been validated in various clinical situations. However, it has not been investigated during a short stay in the intensive care unit (ICU). This study aimed to evaluate the association between the SOFA score and outcomes in patients who were monitored for less than one day after non-cardiac surgery. Methods: From a total of 203,787 consecutive adult patients who underwent non-cardiac surgery between January 2011 and June 2019, we selected 17,714 who were transferred to the ICU immediately after surgery and stayed for less than 24 h. Patients were divided according to quartile value and change between the initial and follow-up levels of SOFA score. Results: Three-year mortality tended to increase with a higher initial SOFA score (11.7%, 11.8%, 15.1%, and 17.8%, respectively). The patients were divided according to changes in the SOFA score at the midnight postoperative follow-up check: 16,176 (91.3%) in the stable group and 1538 (8.7%) in the worsened group. The worsened group showed significantly higher three-year mortality and complications (13.2% vs. 18.6%; HR [hazard ratio]: 1.236; 95% CI [confidence interval]: 1.108–1.402; p £ 0.0021 for three-year mortality and 3.8% vs. 9.1%; HR: 2.13; 95% CI: 1.73–2.60; p < 0.001 for acute kidney injury). Conclusions: The SOFA score during a short stay in the ICU after non-cardiac surgery showed an association with mortality. The change in SOFA score may need to be considered at discharge from the ICU.