Purpose: This study was performed to identify the risk of mortality in patients diagnosed with human epidermal growth factor receptor 2 (HER2)-positive ductal carcinoma in situ (DCIS). Methods: We selected 2,592 patients with HER2-positive DCIS from Korean Breast Cancer Society (KBCS) database between January 1997 and December 2019. Patients who received neoadjuvant chemotherapy were excluded. Logistic regression analysis was used to determine the association between clinical factors and overall death after adjusting for tumor and clinical characteristics. Mortality data were modified using the Statistics Korea data. Results: Thirty deaths (1.2%) were identified out of 2,592 patients in the KBCS database. In the univariate logistic regression analysis, older age, higher body mass index (BMI), type of breast surgery (mastectomy), estrogen receptornegative, progesterone receptor-negative, and exposure to endocrine therapy were significant clinical factors associated with death. In the multivariate analysis, age (hazard ratio [HR], 1.062; 95% confidence interval [CI], 1.015–1.111; P = 0.006), BMI (HR, 1.179; 95% CI, 1.032–1.347, P = 0.016), breast surgery type (mastectomy vs. lumpectomy; HR, 0.285; 95% CI, 0.096–0.844; P = 0.024), and endocrine therapy (HR, 0.314; 95% CI, 0.099–0.995; P = 0.049) were significant risk factors for mortality. Conclusion Advanced age, higher BMI, mastectomy, and the absence of endocrine therapy were factors associated with poor survival of patients with HER2-positive DCIS. This finding requires further validation combined with additional analysis of large databases.