The temporal discrimination paradigm requires subjects to compare the duration of a probe stimulus to that of a sample previously stored in working or long-term memory, thus providing an index of timing that is independent of a motor response. However, the estimation process itself comprises several component cognitive processes, including timing, storage, retrieval, and comparison of durations. Previous imaging studies have attempted to disentangle these components by simply measuring brain activity during early versus late scanning epochs. We aim to improve the temporal resolution and precision of this approach by using rapid event-related functional magnetic resonance imaging to time-lock the hemodynamic response to presentation of the sample and probe stimuli themselves. Compared to a control (color-estimation) task, which was matched in terms of difficulty, sustained attention, and motor preparation requirements, we found selective activation of the left putamen for the storage (“encoding”) of stimulus duration into working memory (WM). Moreover, increased putamen activity was linked to enhanced timing performance, suggesting that the level of putamen activity may modulate the depth of temporal encoding. Retrieval and comparison of stimulus duration in WM selectively activated the right superior temporal gyrus. Finally, the supplementary motor area was equally active during both sample and probe stages of the task, suggesting a fundamental role in timing the duration of a stimulus that is currently unfolding in time.