The ameliorative effect of fulvic acid (0, 300, and 600 mg L− 1) on photosystem II and antioxidant enzyme activity of the rapeseed (Brassica napus L.) plant under water stress (60, 100, and 140 mm evaporation from class A pan) was studied using split plots in a randomized complete block design with three replications. Results indicated that application of fulvic acid (FA) improved the maximum quantum efficiency of PSII (Fv/Fm) and performance index (PI) of plants under both well-watered and limited-water conditions. The time span from Fo to Fm and the energy necessary for the closure of all reaction centers was significantly increased, but the size of the plastoquinone pool was reduced with increasing water stress levels. Plants treated with FA had higher peroxidase and catalase activities under all irrigation conditions. Activities of ascorbate peroxidase and superoxide dismutase in plants increased with increasing water stress. Malondialdehyde increased under severe water stress, but application of FA significantly decreased lipid peroxidation. Production of reactive oxygen species (ROS) is a common phenomenon in plants under stress. Under this condition, the balance between the production of ROS and the quenching activity of antioxidants is upset, often resulting in oxidative damage. In this study, application of FA significantly increased fluorescence of chlorophyll a, inhibiting ROS production and enhancing antioxidant enzymes activity that destroyed ROS. Thus, ROS in plant cells was reduced under water stress by application of FA and consequently lipid peroxidation was reduced.