Here, we review recent transcranial magnetic stimulation studies and investigations in patients with neurological disease such as Parkinson's disease and stroke, showing that the neural processing of time requires the activity of wide range-distributed brain networks. The neural activity of the cerebellum seems most crucial when subjects are required to quickly estimate the passage of brief intervals, and when time is computed in relation to precise salient events. Conversely, the circuits involving the striatum and the substantia nigra projecting to the prefrontal cortex (PFC) are mostly implicated in supra-second time intervals and when time is processed in conjunction with other cognitive functions. A conscious representation of temporal intervals relies on the integrity of the prefrontal and parietal cortices. The role of the PFC becomes predominant when time intervals have to be kept in memory, especially for longer supra-second time intervals, or when the task requires a high cognitive level. We conclude that the contribution of these strongly interconnected anatomical structures in time processing is not fixed, depending not only on the duration of the time interval to be assessed by the brain, but also on the cognitive set, the chosen task and the stimulus modality.