Selenium (Se) is a micronutrient for humans and other animals; however, it can cause severe toxicity at high concentrations. Selenium and sulfur (S) present a strict relationship in plants and soils, affecting their uptake and accumulations. Thus, addressing selenium-sulfur interaction is important to understand selenium nutrition and toxicity in plants, which could influence crop composition and production, and the toxicity risk to humans and animals. Here, we aimed to evaluate the impact of selenium exposure on rice plants grown under different sulfur supplies at tillering and grain ripening phases. We studied the effects of selenate and sulfate doses on rice plants grown hydroponically or in soils with varying clay contents. In the hydroponic experiment (short-term experiment), rice plants were grown until tillering stage under combinations of two concentrations of Se (0 and 20 µM Se) and S (0.1 and 0.5 mM S) in the nutrient solution. In the long-term, rice plants were grown until the ripening stage in two Oxisols with different clay contents (240 and 620 g kg−1 clay) under combinations of five doses of Se (0; 0.5; 1.0; 2.0 and 4.0 mg dm−3 Se) and three doses of S (0; 45; and 90 mg dm−3 S). We also performed sorption assays to evaluate the influence of soil clay content (240 and 620 g kg−1 clay) and S doses (0; 45; and 90 mg dm−3 S) on selenate adsorption and desorption at exposure to 4.0 mg kg−1 Se. Sulfate supply alleviated selenate toxicity in both short-term and long-term experiments. Selenate treatment up-regulated the expression of sulfate transporters (OsSULTR1;1 and OsSULTR1;2), leading to increased sulfur contents in rice seedlings, which enhanced the antioxidant system (catalase and ascorbate peroxidase activities and glutathione content) and alleviated selenate toxicity. However, this enhanced mechanism is absent in seedlings grown under a low sulfur supply, presenting severe Se toxicity. Moreover, soil clay contents strongly influenced selenate availability. The higher clay content promoted a high selenate adsorption capacity (67% of Se added), resulting in lower selenium contents in shoots and grains and the absence of toxicity symptoms. In contrast, a lower clay content presented a low selenate adsorption capacity (24% of Se added), increasing the Se availability, which can favor the biofortification of crops. However, high selenate doses caused growth and yield impairment in rice cultivated in the soil with lower selenate adsorption, which exhibited higher Se concentrations in shoots and grains, increasing the risk of Se toxicity for humans and animals.