Water pollution has become one of the major global issues, posing serious threat to both humans and aquatic life. The elimination of organic industrial pollutants from wastewater is currently a major area of research. Herein, we report for the first time a novel FeSe2/ZnO composite system for highly efficient removal of organic dyes under visible light. FeSe2/ZnO composites with varying mass ratios of FeSe2 were successfully prepared through simple and low-cost chemical method. The physiochemical properties of the prepared FeSe2/ZnO composites were carefully evaluated and compared with those of pure ZnO rods and FeSe2 flowers. UV–vis spectroscopy confirmed that the coupling of FeSe2 with ZnO caused a significant improvement in the optical absorption of ZnO. The bandgap energies of FeSe2/ZnO composites showed a red shift with increasing the ratio of FeSe2 flowers. The prepared samples were evaluated for their photocatalytic response against the removal of methylene blue dye. Compared to the pure FeSe2 and ZnO, the composites displayed impressive photocatalytic performance. Among the prepared samples, composite with an optimum ratio of 75 wt% FeSe2 revealed outstanding photocatalytic efficiency, making it a promising candidate for the removal of organic pollutants.