Abstract Background Nucleobindin 2 (NUCB2) abnormal expression has been reported in gastric cancer and breast cancer. However, the role of NUCB2 in prostate cancer (PCa) remains unclear. The aim of the present study was to investigate the NUCB2 expression in PCa tissues and adjacent non-cancerous tissues and its potential relevance to clinicopathological variables and prognosis. Methods NUCB2 mRNA expression was determined by real-time quantitative real time reverse transcriptase polymerase chain reaction in 180 pairs of fresh frozen PCa tissues and corresponding non-cancerous tissues. Kaplan-Meier analysis and Cox proportional hazards regression models were used to investigate the correlation between NUCB2 expression and prognosis of PCa patients. Results Our results showed that the expression level of NUCB2 mRNA in PCa tissues was significantly higher than those in non-cancerous tissues. Our results indicated that the high expression of NUCB2 in PCa was associated with lymph node metastasis, preoperative PSA, Gleason score, and angiolymphatic invasion. Kaplan–Meier survival analysis showed that patients with high NUCB2 expression have shorter biochemical recurrence (BCR)-free survival time compared to patients with low NUCB2 expression. Multivariate analysis revealed that NUCB2 expression was an independent predictor of BCR-free survival. Conclusions NUCB2 might play a positive role in PCa development and could serve as an independent predictor of BCR-free survival.