Excimer laser coronary atherectomy (ELCA) is an effective treatment to remove intracoronary thrombi. In the present study, we compared in-hospital mortality in patients with acute myocardial infarction (AMI) who underwent conventional treatment and conventional treatment plus ELCA. Among 656 patients who were admitted to our hospital through the Tokyo CCU Network, 104 patients with AMI who were treated by percutaneous coronary intervention between January 2013 and December 2016 met inclusions criteria and underwent conventional treatment with ELCA (ELCA group) and 89 underwent conventional treatment alone (conventional group). We retrospectively evaluated in-hospital mortality within 30 days and used propensity score (PS) matching to reduce assignment bias and multivariate analysis to detect the predictors of in-hospital mortality. In-hospital mortality rate was significantly lower in the ELCA group before and after PS matching (2.9% vs. 13.5%, p = 0.006 before PS matching, and 2.8% vs. 14.1%, p = 0.016 after PS matching). After PS matching, β-blocker or statins use, incidence of shock, Killip classification, and door-to-balloon time were not significantly different. A multivariate logistic regression analysis identified ELCA, dyslipidemia, shock, and left ventricular ejection fraction as independent predictors of in-hospital mortality (odds ratio (OR), 0.147, 95% confidence interval [CI], 0.022–0.959, p = 0.045; OR, 0.077, 95% CI, 0.007–0.805, p = 0.032; OR, 6.494, 95% CI, 1.228–34.34, p = 0.028; OR, 0.890, 95% CI, 0.828–0.957, p = 0.002, respectively). Our data indicate that ELCA with the small diameter and low level emission may reduce the in-hospital mortality compared to conventional methods in patients with AMI in drug-eluting stent era.