MicroRNA (miR)-539 has inhibitory effects on certain types of cancer, but its role in pancreatic cancer (Pca) remains unclear. The present study investigated the effects of miR-539 on Pca, and aimed to determine possible therapeutic targets for the treatment of Pca. The expression of miR-539 in Pca tissues, paired normal adjacent tissues and Pca cell lines (cAPAN-2, BxPc3, cFPAc1, SW1990 and PANc1), and human non-cancerous pancreatic cells (hTRET-HPNE) was determined and compared. The effects of upregulation and downregulation of miR-539 on proliferation, apoptosis, cell cycle, invasion, migration and epithelial-mesenchymal transition (EMT) of Pca cells were investigated. Additionally, the target gene of miR-539 was predicted and its effects on Pca cells were further investigated. The results revealed low expression of miR-539 in Pca tissues and cell lines. Additionally, increasing miR-539 expression inhibited the proliferation, migration, invasion and EMT of Pca cells and induced apoptosis by blocking G1 phase of the cell cycle, while reducing miR-539 expression had the opposite results. Furthermore, specificity protein 1 (SP1) was found to be the target gene of miR-539. SP1 promoted the proliferation, migration, invasion and EMT transformation of Pca cells, but these effects were reversed by high expression of miR-539. Additionally, miR-539 suppressed the proliferation, metastasis, invasion and EMT transformation of Pca cells through targeting SP1. Therefore, miR-539 overexpression may contribute toward development of novel therapeutic strategies for Pca in the future.