TRAF-2 and NCK-interacting kinase (TNIK) is a serine-threonine kinase with a proposed role in Wnt/β-catenin and JNK pathways. Due to its implication in Wnt-mediated colorectal carcinogenesis, selective TNIK inhibition has emerged as an attractive anti-cancer therapeutic strategy. So far, only few TNIK inhibitors have been described and none of them reached advanced preclinical development.In this study, a virtual screening approach was applied for investigation of novel TNIK inhibitors. The best performing ShaEP methodology for similarity searching was applied for screening of a commercially available small molecules database. Among several discovered TNIK kinase inhibitors, a compound containing the furan-2-carboxamide scaffold was found to be the most active, with IC50 = 0.85 µM. An advanced substructure search led to the discovery of a more potent and selective compound with IC50 = 258 nM. The most active compounds were tested in vitro for their effect on Wnt/β-catenin pathway and proliferation of Wnt-active colorectal cancer cells. The compounds identified in this study represent attractive starting points for the development of more potent and selective small molecule TNIK inhibitors for both therapeutic application and research on TNIK biological role.