Indoleamine 2,3-dioxygenase 1 (IDO1) plays an important role in the immune escape of tumors and has emerged as a promising target for cancer immunotherapy. Despite its potential in immuno-oncology, very few chemotypes have been reported to date. Here, we disigned a novel high throughput virtual screening (HTVS) cascade protocol, combining both pharmacophore modeling and molecular docking and it was employed to query commercially available compounds to identify novel inhibitors. Among the 23 compounds selected for the in vitro IDO1 inhibitory activity assay, five compounds exhibit greater than 20% inhibition at a test concentration of 10 µM, with two compounds having an IC value of 23.8 and 8.8 µM, respectively. The novel scaffold together with a ligand efficiency of 0.28 kcal/mol per heavy atom makes both compounds as suitable starting points for future chemistry elaboration. Our HTVS protocol was validated and could be employed in discovery of IDO1 inhibitors.