The neural mechanisms underlying time perception remain elusive. Although the cerebellum (CE) and basal ganglia (BG) are considered fundamental, evidence primarily stems from studies on neurodegenerative diseases, where progressive and widespread damage complicates linking deficits to specific brain structures. In contrast, brain stroke affects focal areas suddenly, allowing for the assessment of immediate functional consequences. Here, we compared patients with acute stroke in the CE and BG to age-matched healthy controls (HC) on both explicit (time bisection, free and 1-second finger tapping) and implicit (rhythmic, temporal orienting) timing tasks. Concerning explicit timing, both CE and BG patients were faster than HC in their free finger tapping, while BG lesions showed greater variability than HC in the 1-second tapping. Similarly, performance on the bisection task suggested deficits more related to cognitive complaints in stroke than specific temporal dysfunction. In implicit timing tasks, BG patients, like HC, effectively used information provided by the rhythm and the temporal orienting cues to anticipate the target onset, whereas CE patients failed and showed longer reaction times. Therefore, before compensatory mechanisms can take effect, acute CE damage might hinder implicit timing, whereas BG lesions could disrupt explicit temporal representation when processed alongside other cognitive functions.