The family with sequence similarity 20, member C (Fam20C), a Golgi casein kinase, has been recently regarded as a potential therapeutic target for the treatment of triple negative breast cancer (TNBC). Lacking enzyme activity center has been becoming an obstacle to the development of small-molecule inhibitors of Fam20C. Herein, we combined in silico high-throughput screening with chemical synthesis methods to obtain a new small-molecule Fam20C inhibitor 3r, which exhibited desired anti-proliferative activities against MDA-MB-231 cells and also inhibited migration. Subsequently, the enzymatic assay, molecular docking, and molecular dynamics (MD) simulations were carried out for validating that 3r could bind to Fam20C. In addition, 3r was found to induce apoptosis via the mitochondrial pathway in MDA-MB-231 cells as well as to inhibit cell migration. Moreover, we demonstrated that 3r inhibited tumor growth in vivo and thereby having a good therapeutic potential on TNBC. Taken together, these results suggest that 3r may be a novel Fam20C inhibitor with anti-proliferative and apoptosis-inducing activities, which would shed light on discovering more small-molecule drugs for the future TNBC therapy. Copyright © 2020 Elsevier Masson SAS. All rights reserved.