Biomphalaria alexandrina snail is the intermediate host of Schistosoma mansoni in Egypt. This study was designed to evaluate the molluscicidal, cercaricidal and miracidicidal activities of thymoquinone bioactive compound from Nigella sativa (TQ), chitosan and thymoquinone loaded with chitosan nanoparticles (TQ/ChNPs). The results proved that thymoquinone bioactive compound from Nigella sativa (TQ) and thymoquinone chitosan and thymoquinone loaded with chitosan nanoparticles (TQ/ChNPs) against B. alexandrina showed no molluscicidal activity was recorded against B. alexandrina snails. On the other hand, the exposure of S. mansoni infected snails to TQ/ChNPs and TQ caused a considerable reduction in the infection percentages and cercarial production/infected treated snail. The average of snail infection in treated groups reached to 30% in comparison with 90.4% in the control group. The results also, showed that thymoquinone loaded with chitosan nanoparticles (TQ/ChNPs) has a promising effect on free larval stages of S. mansoni (miracidia and cercariae).  Cercaricidal and miracidicidal activity of TQ/ChNPs was higher than that of TQ.