Animals and humans make decisions based on their expected outcomes. Since relevant outcomes are often delayed, perceiving delays and choosing between earlier vs. later rewards (intertemporal decision-making) is an essential component of animal behavior. The myriad observations made in experiments studying intertemporal decision-making and time perception have not yet been rationalized within a single theory. Here we present a theory—Training-Integrated Maximized Estimation of Reinforcement Rate (TIMERR)—that explains a wide variety of behavioral observations made in intertemporal decision-making and the perception of time. Our theory postulates that animals make intertemporal choices to optimize expected reward rates over a limited temporal window which includes a past integration interval—over which experienced reward rate is estimated—as well as the expected delay to future reward. Using this theory, we derive mathematical expressions for both the subjective value of a delayed reward and the subjective representation of the delay. A unique contribution of our work is in finding that the past integration interval directly determines the steepness of temporal discounting and the non-linearity of time perception. In so doing, our theory provides a single framework to understand both intertemporal decision-making and time perception.