A recently described auditory tempo perception paradigm revealed individual differences in perceived stimulus timing for identical stimulus sequences. The current study takes advantage of this paradigm by recording event-related potentials (ERPs) concurrent with task performance in order to reveal brain responses that reflect individual differences in timing strategy. No strategy-related differences were observed in sensory encoding of tones, as measured by the P1-N1-P2 complex. However, the contingent negative variation (CNV) leading up to the final tone of the sequence varied as a function of strategy, as did a parietal-maximum late positive component (P3b) that occurred following the final tone. These data suggest that temporal expectancy for and cognitive processing of the final tone of rhythmic sequences underlies differences in strategy during rhythm perception.