Time estimation was investigated in 24 healthy adults, 12 women and 12 men, before and after an exhaustive exercise. We compared the capability of estimating time intervals in the range from 1 to 5 s using tasks requiring mental count and tasks that did not allow the mental count. Time estimation and blood lactate levels were evaluated before and at the end of the exercise. We found that the perception of time intervals between 1 and 5 s was affected at the end of the exercise. The observed effects, associated with a significant increase in blood lactate levels, were different in the two types of time estimation used in the present study. In experimental conditions in which participants had to evaluate duration of the time interval by mental counting, at the end of exercise a significant reduction in the overestimation of time made at rest was observed. On the other hand, when participants had to assess the difference in duration between two events without the possibility to mentally count, at the end of the exercise a significant deterioration in performance was observed. In both cases, no gender differences were seen.