Small ubiquitin like modifier (SUMO) specific proteases (SENPs) are cysteine proteases that carry out the proteolytic processing of SUMO from its pro form as well as the deconjugation of SUMO from substrate proteins. SENPs are attractive targets for drug discovery due to their crucial role in the development of various diseases. However, the SENPs inhibitor discovery efforts were limited, and only a few inhibitors or activity based probes have been identified until now. Here, we report a new class of SENP2 inhibitors identified by a combination of structure based virtual screening and quantitative FRET based assay. Our virtual screening protocol initially involves the identification of small molecules that have similar shape and electrostatic properties with the conjugate of SUMO1 C-terminal residues and substrate lysine. Molecular docking was then used to prioritize these small molecules for a FRET based assay that quantifies their SENP2 endopeptidase activity. The initial round of virtual screening followed by FRET based assay has enabled the identification of eight compounds with >40% SENP2 inhibition at 30 μM compound concentration. Five of these compounds belong to two scaffolds containing a 1,2,5-oxadiazole core that represent a novel class of SENP2 inhibitors. To improve the inhibitory potency and explore the structure-activity relationship of these two 1,2,5-oxadiazole scaffolds, structurally related compounds were identified in another round of virtual screening. The biological assay results confirmed SENP2 inhibitory activity of these two scaffolds. The most potent compound of each scaffold showed an IC50 of 5.9 and 3.7 μM. Most of the compounds also inhibited closely related isoform SENP1, while no detectable inhibition on other proteases, such as papain and trypsin, was observed. Our study suggests that 1,2,5-oxadiazoles could be used as a starting point for the development of novel therapeutic agents against various diseases targeting SENPs.