Which brain sites represent the final form of motor commands that encode temporal patterns of muscle activities? Here, we show the possible brain sites which have activity equivalent to the motor commands with functional magnetic resonance imaging (fMRI). We hypothesized that short-temporal patterns of movements or stimuli are reflected in blood-oxygenation-level-dependent (BOLD) responses and we searched for regions representing the response. Participants performed two temporal patterns of tapping and/or listened to the same patterns of auditory stimuli in a 3T fMRI. The patterns were designed to have the same number (11) of events and the same duration, but different temporal distribution of events. The 11 events were divided into two parts (10 repetitive taps and one stand-alone tap) and the interval of the two parts was 3s. The two patterns had reverse order of the two parts. The results revealed that different temporal patterns of auditory stimuli were represented in different temporal features of BOLD responses in the bilateral auditory cortex, whereas different temporal patterns of tapping were reflected in contralateral primary motor cortex and the ipsilateral anterior cerebellum. In bilateral premotor cortex, supplementary motor area, visual cortex, and posterior cerebellum, task-related BOLD responses were exhibited, but their responses did not reflect the temporal patterns of the movement and/or stimuli. One possible explanation is that the neuronal activities were similar for the two patterns in these regions. The sensitivity of the BOLD response to the temporal patterns reflects local differences in functional contributions to the tasks. The present experimental design and analysis may be useful to reveal particular brain regions that participate in multiple functions.