Gibbon's scalar expectancy theory assumes three processing stages in time estimation: a collating level in which event durations are automatically tracked, a counting level that reads out the time-tracking system, and a comparing level in which event durations are matched to abstract temporal references. Pöppel's theory, however, postulates a dual system for perception of durations below and above 2 s. By testing the neurophysiological plausibility of Gibbon's proposal using functional magnetic resonance imaging, we validate a three-staged model of time estimation and further show that the collating process is duplicated. Although the motor system automatically tracks durations below 2 s, mesial brain regions of the so-called “default mode network” keep track of longer events. Our results further support unique counting and comparing systems, involving prefrontal and parietal cortices in collators' readout, and the temporal cortex in contextual time estimation. These findings provide a coherent neuroanatomical framework for two theories of time perception.