Selenate removal from a water body is being vigorously debated owing to severe health impact, but inhibitions of coexisting anions have been reported. To suggest a viable treatment option, this study investigates the effect of nitrate and perchlorate on selenate reduction in a laboratory-scale sequencing batch reactor. The experimental design tests how competing electron acceptors (NO3− and ClO4−) and electron donor (acetate) limitations affect selenate reduction in the reactor. Results show that the reactor achieves almost complete selenate reduction within the initial concentration ranges of 0.1−1 mM by enriching selenate-reducing bacteria with appropriate temperature (30 °C) and acclimation period (50 days). We monitored simultaneous selenate and nitrate reduction in the reactor without specific inhibition due to a difference in microbial growth strategy related to electron donor status. Lack of perchlorate-reducing bacteria makes perchlorate addition (0.2 mM) not to be closely associated with dissimilative perchlorate reduction. These results provide information that can help us to understand the effect of competing electron acceptors on selenate reduction and the kinetics of potential parallel reactions in the reactor.