Recently, potential anti-cancer compounds are screened for its anti-diabetic activity. Search for anti-diabetic compounds are vital among researchers, as the rise in the number of diabetic patients is increasing day today. In the present study, in silico approach is carried out to find the anti-diabetic activity of two anti-cancer compounds namely Baicalein and Wogonin from Scutellaria baicalensis. These two compounds were examined for anti-diabetic activity by docking against key molecular targets such as alpha glucosidase, alpha amylase, aldose reductase, lipase and nuclear receptors PPARα, PPARγ using PatchDock algorithm. Further, for better refinement FireDock was carried away. The complex binding interaction was defined by the Atomic Contact Energy (ACE) obtained and it was compared with the standard drugs. The effects of the current study clearly show the two bio active compounds, Baicalein and Wogonin, have potent diabetic activity. But which is moderate, when compared with standard drugs.This study illuminates the use of in silico docking for identification of potent anti-diabetic compounds in a short period.