Animals appear to possess an internal timer during action, based on the passage of time. However, the neural underpinnings of the perception of time, ranging from seconds to minutes, remain unclear. Herein, we considered the neural representation of time based on mounting evidence on the neural correlates of time perception. The passage of time in the brain is represented by two types of neural encoding as follows: (i) the modulation of firing rates in single neurons and (ii) the sequential activity in neural ensembles. Time-dependent neural activity reflects the relative time rather than the absolute time, similar to a clock. They emerge in multiple regions, including the hippocampus, medial and lateral entorhinal cortices, medial prefrontal cortex, and dorsal striatum. Moreover, they involve different brain regions, depending on an implicit or explicit event duration. Thus, the two types of internal timers distributed across multiple brain regions simultaneously engage in time perception, in response to implicit or explicit time demands.