Phosphatase of regenerating liver (PRL)-3 is involved in the metastasis of various tumors, but the expression of PRL-3 and its possible role in primary intrahepatic cholangiocarcinoma (ICC) has not been reported yet. In this study, we assessed the expression levels of PRL-3 by immunohistochemistry in 102 primary ICC samples, 62 matched lymph node metastases (LNM) and 102 adjacent normal liver tissues. Then we investigated the relationship between PRL-3 expression and clinicopathologic factors. Survival analysis was performed to determine the prognostic significance of PRL-3 expression in ICC. Immunochemistry results suggested PRL-3 expression was negative or weak in non-neoplastic intrahepatic bile ducts of adjacent liver tissue. In primary lesion and LNM high PRL-3 expression was frequently detected. Furthermore, the rate of high PRL-3 expression in LNM was higher than that in primary lesion (80.6% vs. 47.1%, P < 0.05). High expression of PRL-3 in primary tumors was significantly associated with TNM (P < 0.001), T stage (P < 0.001), vascular invasion (P = 0.002), and LNM (P < 0.001). Survival analysis results with Kaplan-Meier method and Cox proportional hazard model indicated high expression of PRL-3 was correlated with decreased overall survival and was an independent prognostic marker of overall survival. Thus, our results suggested high expression of PRL-3 was correlated with progression and metastasis of ICC and indicated negative prognostic impact. PRL-3 might serve as a novel prognostic marker for patients with ICC.