Entamoeba histolytica is one of the common causes of infection in humans around the world. It causes clinically significant infection due to the fact that it causes morbidity and mortality. There is a need for new and safe drugs in the treatment of amebiasis. In this study, the activity of proton pump inhibitors against this parasite were investigated. Pantoprazole, lansoprazole, omeprazole, esomeprazole and rabeprazole were examined in detail. Initially, related drugs are optimized at M062X/6-31+G(d) level in water. Then, 3JS5, 3IDO and 3ILY were minimized at OPLS3e method. The docking calculations were performed and it is found that pantoprazole could be a significant candidate in the inhibiting of Entamoeba histolytica. Then, the interaction between pantoprazole and the target parasite were examined in the range of 0 – 100 nanoseconds (ns). The interaction energies in each one ns were calculated. As a result, the interaction was found as stronger than 88 ns. Pantoprazole was clinged to Entamoeba histolytica to inhibiting it.