We aimed to investigate the value of breast magnetic resonance (MR) imaging and positron emission tomography-computed tomography (PET/CT) in predicting advanced axillary lymph node (ALN) metastases (ypN2-3) after neoadjuvant chemotherapy (NAC) in invasive ductal carcinoma patients. A total of 108 patients with invasive ductal carcinoma underwent breast MR imaging and PET/CT both before and after NAC (termed initial staging and restaging, respectively). The number of positive ALNs and the short diameter (SD) of the largest ALN on breast MR imaging and maximal standardized uptake value (SUVmax) in the ALNs on PET/CT were evaluated. Odds ratio (OR) for prediction of advanced ALN metastases was calculated. The negative predictive value (NPV) of restaging imaging for exclusion of advanced ALN metastases was also calculated. Patients with advanced ALN metastases were more likely to have a higher number (≥2) of positive LNs (OR, 8.06; P = 0.015) on restaging MR imaging. No clinico-pathological factors were significantly associated with advanced ALN metastases. With restaging MR imaging, PET/CT, and MR imaging plus PET/CT, the NPV for excluding advanced ALN metastases was 97.3%, 94.4%, and 100.0%. A higher number of positive ALNs on restaging MR imaging was an independent predictor for advanced ALN metastases after NAC.