Selaginella tamariscina (ST), a well-known traditional medicinal plant, has been used to treat various cancers, including pancreatic cancer. However, the underlying mechanism by which Selaginellin B, a natural pigment isolated and purified from ST, protects against pancreatic cells has yet to be fully elucidated. In the present study, the biological functions of Selaginellin B were investigated using apoptosis, migration and colony formation assays in ASPC-1 and PANC-1 cells. In addition, apoptosis-associated proteins were detected by Western blotting. Our results demonstrated that Selaginellin B induced apoptosis, as evidenced by the increased cleaved caspase-3 level and Bax/Bcl-2 ratio. Moreover, Selaginellin B led to a marked up-regulation of the ratio of LC3-II/LC3-I in ASPC-1 and PANC-1 cells, respectively. Furthermore, reverse pharmacophore screening, molecular docking and molecular dynamics simulation studies revealed that Janus kinase 2 (JAK2) may be a potential target for Selaginellin B. In summary, the results of the present research have demonstrated that Selaginellin B is an effective anticancer agent against PANC-1 and ASPC-1 cells, and the compound holds great promise for the treatment of pancreatic cancer.