The Go/NoGo variants of the auditory event-related potentials were shown promising for clinical researches; however, prior to the wider application, it is important to evaluate potential modulating factors. We aimed to evaluate gender effect on the behavioral and electrophysiological responses in an auditory equiprobable Go/NoGo task. The auditory equal probability Go/NoGo paradigm with two types of stimuli was presented to 79 healthy subjects (40 females and 39 males, age 18-30 years) during EEG recording. Behavioral performance, latency and amplitude of N2 and P3 waves in the Go and the NoGo conditions were evaluated and compared between genders. The response times did not differ between genders; however, females were less accurate on the task. They also exhibited slower N2s and P3s in both Go and NoGo conditions and higher P3 amplitudes. Our results suggest that females require longer times for monitoring of response conflict (N2s) and outcome inhibition (NoGo-P3) and more neural resources and longer processing times for motor response execution (Go-P3). The research provides evidence that gender factor is important in the Go/NoGo studies employing auditory equiprobable paradigm.