There are controversies in the comparison of overall survival between invasive micropapillary carcinoma of the breast (IMPC) and invasive ductal carcinoma (IDC). The objective of this study was to compare the long‐term survival outcome between non‐metastatic IMPC and IDC. The Surveillance, Epidemiology, and End Results database was searched to identify women with non‐metastatic IMPC and IDC diagnosed between 2001 and 2013. Comparisons of patient and tumor characteristics were performed using Pearson's chi‐square. The propensity score matching method was applied with each IMPC matched to one IDC. Breast cancer‐specific survival (BCSS) and overall survival (OS) were estimated using the Kaplan–Meier product limit method and compared across groups using the log‐rank statistic. Multivariate analysis was performed through Cox models. IMPC was presented with aggressive clinical presentations such as larger tumor, more positive lymph nodes, and more advanced stage compared with IDC. A higher rate of estrogen receptor (ER)/progesterone receptor (PR) positivity was also observed in IMPC. With a median follow‐up of 64 months, IMPC had a better BCSS (P = 0.031) and OS (P = 0.012) compared with IDC. In a case–control analysis IMPC was still an independent favorable prognostic factor for BCSS (HR = 0.410, P < 0.001, 95% CI: 0.293–0.572) and OS (HR = 0.497, P < 0.001, 95% CI: 0.387–0.637). In subgroup analysis, IMPC always showed a better survival outcome compared with IDC except in AJCC stage I and histologic grade I disease. IMPC has a better long‐term survival outcome compared with IDC in spite of its highly aggressive clinical presentation.