Dual-specificity phosphatase 6(DUSP6) downregulates various cellular signaling through the dephosphorylation of extracellular signal-regulated kinase(ERK). DUSP6 has proved to be an effective therapeutic target for the cancer treatment. There was a lot of effort to develop the small-molecule inhibitor that targets the active site pocket of DUSP6. However, these inhibitors have structurally limits with potency, selectivity and membrane permeability. Here, we have been able to identify seven novel allosteric inhibitors of DUSP6 by virtual screening. Allosteric inhibitors target the sites distal from the active site and inhibit the enzyme activity by inducing conformational changes from the allosteric binding site to the active site. These inhibitors revealed high potencies with the associated IC50 values and were screened for having desirable physicochemical properties as a drug candidate. Also, we calculated the enzyme kinetics to determine that the selected inhibitors are allosteric inhibitor. Therefore, we assure that the small molecules deserve a considerable allosteric inhibitor for further development.