BACKGROUND AND PURPOSE: The modified systemic inflammation score (mSIS) system, which is constructed based on the neutrophil to lymphocyte ratio (NLR) and albumin (Alb), has not been applied to evaluate the prognosis of malignant breast cancer patients who underwent neoadjuvant chemotherapy (NAC). The present study aimed to explore the relationship between the mSIS and overall survival (OS), disease-free survival (DFS) and pathological complete response (pCR). METHODS: A total of 305 malignant breast tumor patients who underwent NAC were incorporated into this retrospective analysis. We determined OS and DFS using K-M survival curves and the log-rank test. The relationship between the mSIS and OS and DFS was evaluated by a Cox regression model. A nomogram was constructed based on Cox regression analysis. RESULTS: Patients in the mSIS low-risk group had better 5- and 8-year OS rates than those in the mSIS high-risk group (59.8% vs. 77.0%; 50.1% vs. 67.7%; X = 8.5, P = 0.0035, respectively). Patients in the mSIS (1 + 2 score) + pCR subgroup had the highest 5- and 8-year OS and disease-free survival (DFS) rates (OS: 55.0% vs. 75.7% vs. 84.8, 42.8% vs. 65.7% vs. 79.8%, X = 16.6, P = 0.00025; DFS: 38.8% vs. 54.7% vs. 76.3%, 33.3% vs. 42.3 vs. 72.1%, X2 = 12.4, P = 0.002, respectively). Based on the mSIS, clinical T stage and pCR results, the nomogram had better predictive ability than the clinical TNM stage, NLR and Alb. CONCLUSIONS: mSIS is a promising prognostic tool for malignant breast tumor patients who underwent NAC, and the combination of mSIS and pCR is helpful in enhancing the ability to predict a pCR.