Natural Killer (NK) cells are important in the first response against viruses and tumours. Compounds that modulate human NK cell activity offer interesting prophylactic and therapeutic options, however, a systematic screening tool is lacking. Development of suitable NK cell lines or receptor-based assays is hindered by the highly complicated regulation of the different NK cell subsets by multiple receptors. Here, we describe a cell-based flowcytometric activity assay adapted to identify NK cell modulating compounds. Fresh human peripheral blood mononuclear cells (PBMC) were incubated with NK-sensitive K562 target cells labelled with 5-(6)-carboxyfluorescein succinimidyl ester, followed by DNA-labelling with propidium iodide to identify dead cells. The assay demonstrated a good performance with an average Z′-factor of 0.6 and over 95% of the assays fulfilled the quality criteria, suggesting that it is possible to use a complex system with two different cell types to screen compounds. A large number of (natural) compounds and extracts were tested and normalized to the positive control, Interleukin-2. Promising and less promising compounds were distinguished. Effectiveness of compounds was based on the augmentation of NK cell activity as well as the number of responding subjects. To conclude the assay is robust, reliable and can be used for functional screening of natural compounds modulating NK cell activity.