Background Pathological complete response (pCR) is the ultimate response in breast cancer patients treated with neoadjuvant chemotherapy (NCT). It might be a surrogate outcome for disease-free survival (DFS) and overall survival (OS). We studied the effect of clinical tumor stage (cT-stage) on tumor pCR and the effect of pCR per cT-stage on 5-year OS and DFS. Methods Using the Netherlands Cancer Registry, all primary invasive breast cancer patients treated with NCT from 2005 until 2008 were identified. Univariable logistic regression analysis was performed to evaluate the effect of cT-stage on pCR, stepwise logistic regression analysis to correct for potential confounders and Kaplan–Meier survival analyses to calculate OS and DFS after five years. Results In 2366 patients, overall pCR rate was 21%. For cT1, cT2, cT3, and cT4, pCR rates were 31, 22, 18, and 17%, respectively. Lower cT-stage (cT1-2 vs cT3-4) was a significant independent predictor of higher pCR rate ( p  < 0.001, OR 3.15). Furthermore, positive HER2 status ( p  < 0.001, OR 2.30), negative estrogen receptor status ( p  = 0.062, OR 1.69), and negative progesterone receptor status ( p  = 0.008, OR 2.27) were independent predictors of pCR. OS and DFS were up to 20% higher in patients with cT2-4 tumors with pCR versus patients without pCR. DFS was also higher for cT1 tumors with pCR. Conclusions The most important predictor of pCR in breast cancer patients is cT-stage: lower cT-stages have significantly higher pCR rates than higher cT-stages. Patients with cT2-4 tumors achieving pCR have higher OS and DFS compared to patients not achieving pCR.