SYNTAX Score II (SSII) connects clinical variables with coronary anatomy. We investigated the prognostic value of SSII in patients with ST segment elevated myocardial infarction (STEMI) complicated with cardiogenic shock treated with primary percutaneous coronary intervention (PPCI). In this retrospective analysis, we evaluated the in-hospital prognostic impact of SSII on 492 patients with STEMI complicated with cardiogenic shock treated with PPCI. Patients were stratified by tertiles of SSII, in-hospital clinical outcomes were compared between those groups. In-hospital univariate analysis revealed higher rates of in-hospital death for patients with SSII in tertile 3, as compared to patients with SSII in tertile 1 (OR 17.4, 95% CI 10.0–30.2, p < 0.001). After adjustment for confounding baseline variables, SSII in tertile 3 was associated with 6.2-fold hazard of in-hospital death (OR 6.2, 95% CI 2.6–14.1, p < 0.001). SSII in patients with STEMI complicated with cardiogenic shock treated with PPCI provide an independent prognostic marker of in-hospital outcomes. Our data suggests SSII to be a simple, feasible and clinically applicable tool for rapid risk stratification in patients with STEMI complicated with cardiogenic shock treated with PPCI.