Selenium (Se) supplementation has been shown to attenuate the detrimental effects of abiotic stress conditions, such as salinity and drought on plant growth and development. However, little is known about Se-related responses in plants exposed to boron (B) toxicity. In this study, we aimed to evaluate the effects of Se supplementation on growth, B content, photosynthetic pigment concentrations, compatible solutes content, oxidative damage, and antioxidant capacity in pepper plants grown under low and high B stress. In order to achieve this objective, 26 day-old pepper plants were treated with different concentrations of boric acid (2 and 4 mM) and/or sodium selenate (10 and 20 µM) for 14 days. Our results show that both low and high B stress cause growth inhibition and oxidative injury in pepper. Furthermore, B stress resulted in significant increases in APX, POD, and SOD activities as well as in proline, reducing sugar, and total sugar contents at both levels. Lastly, a marked decrease was observed in photosynthetic pigment and total flavonoid contents in pepper leaves subjected to B toxicity. Se application at 10 µM alleviated low B stress-induced growth inhibition and lipid peroxidation by decreasing B accumulation and enhancing chlorophyll content in pepper. In addition, Se supplementation decreased the accumulation of soluble sugar and proline in B-treated pepper leaves. In conclusion, our findings reveal that Se application is protective against the adverse effects of B toxicity on growth and oxidative metabolism in pepper.