Fenhexamid is one of the most extensively used fungicides against several plant pathogens. The green alga Chlorella vulgaris can be used as a model organism for toxicological tests in aquatic environments. The toxicity of fenhexamid was evaluated and the sub-lethal concentrations (LC10, LC25, and LC50) were determined after 24, 48, and 96h of exposure. The physiological responses of C. vulgaris to fenhexamid exposure including growth, photosynthetic efficiency, as well as antioxidant activities were used to investigate its impacts on aquatic organisms. The results showed a high reduction in cell number of C. vulgaris in a concentration-dependent manner, with maximum reduction up to 62.9% after 96h exposure to 120 µg. L−1 fenhexamid. Also, a remarkable decrease in the concentration of chlorophyll a, b and total chlorophyll with 2.04, 1.06, and 2.3-fold time, respectively. The content of antioxidant enzymes elevated after exposure to fenhexamid, indicating the oxidative damage in the algal cell after treatment. The activity of GSH, MDA, and SOD enzymes elevated by 41.3%, 82.8%, 65.3% respectively, after 96h exposure to 120 µg. L−1 fenhexamid, While the content of POD and CAT enzymes increased by 56.1% and 58%, respectively after 24h of exposure. Examination by electron microscopy shows high damage in the cytomembrane and the cell wall in addition to increasing in size and number of the starch granules which indicate high stress associated with exposure to the tested fungicide. Therefore, preventing or at least reducing the broad use of fenhexamid as a fungicide becomes an urgent necessity to protect aquatic organisms.