Pitch plays a crucial role in music and speech perception. Pitch perception is characterized by multiple perceptual dimensions, such as pitch height and chroma. Information provided by auditory signals that are related to these perceptual dimensions can be either congruent or incongruent. To create conflicting cues for pitch perception, we modified Shepard tones by varying the pitch height and pitch chroma dimensions in either the same or opposite directions. Our behavioral data showed that most listeners judged pitch changes based on pitch chroma, instead of pitch height, when incongruent information was provided. The reliance on pitch chroma resulted in a stable percept of upward or downward pitch shift, rather than alternating between two different percepts. Across the incongruent and congruent conditions, consistent activation was found in the bilateral superior temporal and inferior frontal areas. In addition, significantly stronger activation was observed in the inferior frontal areas during the incongruent compared to congruent conditions. Enhanced functional connectivity was found between the left temporal and bilateral frontal areas in the incongruent than congruent conditions. Increased intra-hemispheric and inter-hemispheric connectivity was also observed in the frontal areas. Our results suggest the involvement of the frontal lobe in top-down and bottom-up processes to generate a stable percept of pitch change with conflicting perceptual cues.