Background: Parasitic infections are a major difficulty in tropical and subtropical countries. Traditionally medicinal plants have been used in folk medicine to treat parasitic infections and are a valuable source of novel anti-parasitics. Objective: In our search for therapeutic alternatives to anti-protozoal chemotherapy, thymoquinone, the active ingredient of Black cumin (Nigella sativa) was examined. Materials and Methods: Thymoquinone was tested against Entamoeba histolytica and Giardia lamblia using in vitro susceptibility assays and the mortality of the parasites were then obtained using the standard calculations. The compound was also tested for 48 and 72 hours on both parasites. Results: The current study indicate that the mortality of TQ showed 85.5%, 91.5% and 96.8% mortality on E. histolytica for 25 ppm at 24 hr, 48 and 72 hr, respectively, with IC 50 2¥10-19 ,. On the other hand, this natural compound showed a mortality of 82.83%, 91.76% and 96.62% mortality on G. lamblia for 25 ppm at 24 hr, 48 and 72 hr, respectively, with IC 50 4.8¥10-5. Metrondizole powder gave 70.9% mortality at 156 ppm at the same times. Conclusion: The current results indicate that TQ is more potent on E. histolytica compared to G. lamblia. Further pharmacological studies were needed to help in the clinical presentation of thymoquinone.