Background: Limited data is present regarding long-term outcomes in chronic kidney disease (CKD) patients presenting with stent thrombosis (ST). We evaluated the possible implications of CKD on long-term mortality in patients presenting with ST-segment elevation myocardial infarction (STEMI) and treated with primary percutaneous coronary intervention (PCI), and its interaction with the presence of ST. Methods: We retrospectively studied 1,722 STEMI patients treated with primary PCI. Baseline CKD was categorized as an estimated glomerular filtration rate <60 mL/min/1.73 m2 at presentation. The presence of ST was determined using the Academic Research Consortium definitions. Patients were evaluated for the presence of CKD and ST, as well as for long-term mortality. Results: A total of 448/1,722 (26%) patients had baseline CKD. Patients with CKD were older and had more comorbidities and a higher rate of ST (4 vs. 7%, respectively, p < 0.001). In a univariate analysis, long-term mortality was significantly higher among those with CKD compared to those without CKD (17.6 vs. 2.7%, p < 0.001). The presence of ST did not alter long-term mortality in both CKD and no-CKD patients. In a Cox regression model, CKD was an independent predictor of long-term mortality (hazard ratio 2.04, 95% confidence interval 1.17-3.56, p = 0.01), while ST as a covariate was not significantly associated with long-term mortality. Conclusion: Among STEMI patients, CKD, but not ST, is a predictor of long-term mortality.