BackgroundSquamous cell carcinoma (SCC) of the breast is a rare malignancy. The clinicopathological features, treatment patterns and prognosis of SCC of the breast is still unclear.MethodsIn this study, we performed a 1:4 SCC-IDC (infiltrating ductal carcinoma) matching analysis of patients diagnosed between 2004 and 2014, using the data from the national cancer database. We used Chi-square test to compare the clinicopathological features and treatment patterns between SCC (n = 686) and IDC (n = 2744) patients. We used Kaplan-Meier analysis and Cox-regression to estimate the survival of SCC and IDC patients.ResultsWe observed that SCC patients are more likely to have T3–4, grade III, and ER negative diseases, when compared to IDC patients. Breast conserving surgery (BCS) (58.3% vs 65.4%, p = 0.048), as well as radiotherapy after BCS (65.3% vs. 83.0%, p < 0.001), was less performed in SCC patients. Among low-risk patients, chemotherapy was used more often for SCC patients (42.9%) than for IDC (18.7%) patients (p = 0.002). In HR-positive patients, endocrine therapy was used less often for SCC patients (51.6%) than for IDC patients (70.5%) (p < 0.001). SCC (vs. IDC) was associated with no responses to neoadjuvant chemotherapy (20% vs. 5.05%, p = 0.019). Adjusted analysis confirmed that SCC (vs. IDC) was associated with worse OS (HR = 1.40, 95%CI 1.17–1.67, P < 0.01), after a median follow-up of 58.3 months. In SCC patients, HR status is not prognostic of OS, but endocrine therapy was significantly associated with improved OS in HR-positive SCC patients.ConclusionsWe conclude that SCC is associated with poorer clinicopathological features, no responses to neoadjuvant chemotherapy and worse clinical outcomes than IDC. The treatment patterns for SCC and IDC are different. Endocrine therapy is necessary for HR-positive SCC patients.Electronic supplementary materialThe online version of this article (10.1186/s12885-018-5212-x) contains supplementary material, which is available to authorized users.