Even though the relationship between syntax score (SS) and coronary no-reflow phenomenon has been studied, the relation between SS and syntax score II (SS II) in patients with no-reflow phenomenon is unknown. We aimed to define the relationship between coronary no-reflow phenomenon and SS II as compared with SS. This study enrolled 193 patients undergoing primary percutaneous coronary intervention for ST elevation myocardial infarction in whom 42 patients developed the no-reflow phenomenon. SS and SS II were calculated in all patients. Bland Altman analysis was used to compare receiver-operating characteristic (ROC) curve analysis results. SS and SS II values were significantly higher in the no-reflow group than the reflow group (28.3 ± 5.5 vs. 18.8 ± 10.1; p < 0.001 and 42.5 (22.1–58.5) vs. 26.1 (13–49.8); p < 0.001 respectively). SS II value >32.3 yielded an area under the curve value of 0.881 (95% CI 0.820–0.942; p < 0.001) and independently predicted no-reflow with a sensitivity of 88% and a specificity of 80% (OR 1.150, 95% CI 1.047–1.263, p = 0.003). Comparison of ROC curve results with Bland Altman analysis showed that area under curve of SS II was larger than that of SS (0.881 vs. 0.785, p = 0.01). SS II may be a more useful tool than SS for prediction no-reflow phenomenon after primary percutaneous coronary intervention in patients with ST elevation myocardial infarction.