Perception of time on the order of seconds (interval timing) is an essential component of cognition, but little is known about the neural mechanism for time perception. In interval timing-related tasks, the animal is required to maintain working memory of the elapsed time from past events and make decisions about when to anticipate future sensory events or to execute motor actions. The prefrontal cortex (PFC) is known to be crucial for working memory and decision making. Although many PFC neurons exhibit memory- and decision-related activity, how interval timing is encoded in PFC neural activity is not yet well understood. Here we show that in rats trained to estimate timing on the order of seconds, many PFC neurons exhibit sustained spiking activity with a variety of temporal profiles of firing rate modulation. Interestingly, in tasks involving different timing, each neuron exhibited the same modulation profile that was temporally scaled by a factor linearly proportional to the task timing. The behavioral variability across trials within each task is also correlated with the inter-trial variability of the temporal scaling factor. Furthermore, cocaine intake, which caused a significant change in timing perception at the behavioral level, led to a corresponding change in the temporal scaling of PFC firing rate modulation. Together, these results point to temporally scalable firing rate modulation as a general mechanism for the neural representation of interval timing during animal behavior.