The application of synthetic algaecides for the control of algae produces by-products that are sometimes toxic to the environment. There is a need for natural and cheap alternatives to synthetic algaecides. In the present study, we investigated the potential of aqueous crude extract of Azadirachta indica to inhibit the growth of Scenedesmus quadricauda. Phytochemical screening of the extract revealed the presence of groups of bioactive compounds that are capable of inhibiting microalgal growth. Chlorophyll a concentration, dry weight production and cell density of microalga decreased with increasing crude extract concentration. After three days of exposure, the 1000 mg/L extract concentration resulted in complete growth inhibition and cell lysis. Furthermore, the ability of S. quadricauda to form multi-celled coenobial structures was compromised in a concentration dependent manner. In general, catalase and peroxidase activities of the microalga were upregulated with increasing extract concentration. These results imply that aqueous neem extract may provide a cheap and ecofriendly alternative for the control of microalgae in aquatic ecosystems.