Radiologically identified para-aortic lymph node (PALN) metastasis is contraindicated for pancreatic cancer (PC) surgery. There is no clinical consensus for unexpected intraoperative PALN. To analyse the prognostic role of unexpected PALN in resectable PC, we retrospectively reviewed data of 1,953 PC patients in a single tertiary centre. Patients with intraoperative PALN without radiological PALN (group A1, negative pathology, n = 59; group A2, positive pathology, n = 13) showed median overall survival (OS) of 24.6 (95% confidence interval [CI]: 15.2–33.2) and 13.0 (95%CI: 4.9–19.7) months, respectively. Patients with radiological PALN metastasis without other metastases (group B, n = 91) showed median OS of 8.6 months (95%CI: 7.4–11.6). Compared with group B, groups A1 and A2 had hazard ratios (HRs) of 0.37 (95%CI, 0.2–0.6) and 1.04 (95%CI: 0.7–1.4), respectively. Compared with group A2, group A1 had HR of 0.33 (95%CI: 0.2–0.7). Analysing regional lymph nodes (LNs), the positive LN ratio affected survival (HR: 2.67, 95%CI: 1.6–4.5), while the absolute number of positive LNs (HR: 1.79, 95%CI: 0.7–4.6) did not. Thus, unexpected malignant PALN has a negative prognostic impact comparable to radiological PALN metastasis. Prompt pathologic evaluation for unexpected PALN and maximal harvest of regional LNs during PC surgery are suggested.