Approximately up to 200 million new cases of infections caused by viruses of the Flaviviridae family, like hepatitis C virus (HCV), West-Nile virus (WNV), dengue virus (DENV) and Japanese encephalitis virus (JEV) are registered annually. Up to date, there is no effective antiviral therapy directed against Flaviviridae viruses. For the replication of all viruses the intact function of nonstructural proteins is necessary. The blockade of their activities leads to inhibition of the virus propagation. Thus, the nucleotide triphosphatase (NTPase) as well as helicase activities of NS3 and the RNA-dependent RNA polymerase (RdRp) activity of NS5 (or NS5B) appear to be exceptionally attractive targets for antiviral compounds. In this context, a systematic screening of chemical libraries and computational analysis are necessary which will lead to the development of effective inhibitors of the Flaviviridae replication complex. In this review the most promissing methods based on different techniques to quantify the enzymatic activities, like radioactivity, fluorescence, colorimetry as well as a coupled second enzymatic reaction are summarized and discussed. These methods serve as a starting point to establish a high throughput system (HTS) that permits more efficient screenings.