Imaging studies have indicated that males and females differ anatomically in brain regions thought to underlie language functions. Functional studies have corroborated this difference by showing gender differences in terms of language processing with females relying on less lateralized processing strategies than males. Gender differences in musical functions might show similar differences in functional asymmetries, although no detailed study has been performed. The current study employed a pitch memory task while acquiring functional magnetic resonance images to investigate possible differences in hemispheric processing between males and females. Gender differences were found in the time course of activation (during the first four imaging time points after the end of the auditory stimulus—“perceptual phase”—and the subsequent three imaging time points after the end of the auditory stimulus—“memory phase”) in both anterior and posterior perisylvian regions. Male subjects had greater lateralized activations (left > right) in anterior and posterior perisylvian regions during the “perceptual” as well as during the “memory” phase. There was a trend for males to have more cerebellar activation than females. Females showed more prominently posterior cingulate/retrosplenial cortex activation compared to males. Although activation patterns differed, there was no difference in the behavioral performance between both genders. These data indicate that similar to language studies, males rely more on left lateralized hemispheric processing even for basic pitch tasks.