The discovery of potent therapeutic compounds against dengue virus is urgently needed. The NS2B-NS3 protease (NS2B-NS3 pro) of dengue fever virus carries out all enzymatic activities needed for polyprotein processing and is considered to be amenable to antiviral inhibition by analogy. Virtual screening of 300,000 compounds using Autodock 3 on the GVSS platform was conducted to identify novel inhibitors against the NS2B-NS3 pro. Thirty-six compounds were selected for in vitro assay against NS2B-NS3 pro expressed in Pichia pastoris. Seven novel compounds were identified as inhibitors with IC 50 values of 3.9 ± 0.6–86.7 ± 3.6 μM. Three strong NS2B-NS3 pro inhibitors were further confirmed as competitive inhibitors with K i values of 4.0 ± 0.4, 4.9 ± 0.3, and 3.4 ± 0.1 μM, respectively. Hydrophobic and hydrogen bond interactions between amino acid residues in the NS3 pro active site with inhibition compounds were also identified.