Entamoeba being an internal parasite is the causative organism of many human and animal infections with lethal consequences. Chemotherapy against Entamoeba was well established by both synthetic and natural products. Vigorous attainments were made by different researchers all over the world for discovering better chemical entities and the potent formulations. Preexisting compounds were developed into non-cytotoxic and with an enhanced therapeutic compounds by usage of multiparametric optimization techniques like QSAR, and molecular docking. The present review is therefore an aerial perspective of importance of medicinal chemistry in anti-amoebic chemotherapy. The review elucidates the existing synthetic compounds, their analogues, natural products, in silico studies and some novel methods adopted for the drug design as anti-amoebic agents which would be of assured benefit in the future drug design.