Pure mucinous breast carcinoma (PMBC) accounts for approximately 2% of all breast carcinoma. Overexpression or amplification of human epidermal growth factor receptor 2 (HER2) is rarely observed in PMBC. We retrieved 119 PMBCs, which included 12 HER2-positive PMBCs and 107 HER2-negative PMBCs, to compare the clinicopathologic features between HER2-positive and HER2-negative neoplasms. The assessed parameters included patient age, menstruation, laterality, tumor size, lymph node status, tumor-node-metastasis (TNM) stage, nuclear grade, receptor status, treatment and prognostic features. HER2-positive PMBCs represented approximately 10.1% of the PMBCs examined. HER2-positive PMBCs showed more frequent lymph node metastasis (P=0.038), a significantly higher clinical TNM stage (P<0.001) and nuclear grade (P<0.001), lower estrogen receptor (ER) and progesterone receptor (PR) expression and higher Ki67 expression than the HER2-negative group (P=0.011, P=0.005, and P=0.001, respectively). HER2-positive PMBCs (untreated with HER2-targeted therapy) had a significantly lower overall survival (OS) rate than HER2-negative PMBCs (P=0.005). Nodal metastasis, higher TNM stage and nuclear grade were identified as factors that result in poorer OS of patients with PMBCs (P<0.001, P=0.016, P<0.001, and P<0.001, respectively). Univariate and multivariate Cox analyses confirmed that HER2 status was an independent prognostic factor for PMBCs (P=0.003 and P=0.012, respectively). HER2-positive PMBC is a rare subtype of breast carcinoma with aggressive biological behavior. It is important to identify tumors with these aggressive clinical behaviors and manage them differently. To the best of our knowledge, this study represents the first systematic investigation of the clinicopathologic features of HER2-positive PMBCs.