New treatments are urgently needed to combat the increasing number of dengue fever cases in endemic countries as well as amongst a large number of travellers from non-endemic countries. Of the 10 virus encoded proteins, NS3 (non-structural 3) and NS5 carry out all the enzymatic activities needed for polyprotein processing and genome replication, and are considered to be amenable to antiviral inhibition by analogy with successes for similar targets in human immunodeficiency virus and hepatitis C virus. The multifunctional NS3 protein of flavivirus forms a non-covalent complex with the NS2B cofactor and contains the serine-protease activity domain at its N-terminus that is responsible for proteolytic processing of the viral polyprotein and a ATPase/helicase and RNA triphosphatase at its C-terminal end that are essential for RNA replication. In addition, NS3 seems to be also involved in virus assembly. This review covers the recent biochemical and structural advances on the NS2B-NS3 protease-helicase and presents an outlook for the development of small molecules as antiviral drugs targeting this fascinating multifunctional protein.