Better methods are needed to improve validity and reliability of physical activity (PA) assessment instruments. The purpose of this study was to compare individual's Borg's Rate of Perceived Exertion (RPE) scores to GT1M ActiGraph accelerometer output, with the aim to better understand estimates of perceived exertion for exercise prescription. Adults were recruited (n = 117) from Utah, with 43.1% males (n = 50), and most (53.1%) self-reporting regular exercise. Participants performed three indoor laps of increasing intensity, ranging from walking to running, and immediately completed a RPE form. A subsample was mailed the same RPE survey 6-8 weeks later to compare differences from their initial responses. Individual accelerometer data was compared to RPE levels from validated metabolic equivalents (METs). There were significant differences between the RPE ratings and the accelerometer output overall for gender (χ(2) = 10.9, P = 0.004), and exercise status (χ(2) = 15.5, P < 0.001). The odds of underestimating RPE for an exerciser were 3.67 times greater than a non-exerciser (95% CI = 1.48, 9.11). The subsample also underestimated RPE after the time lapse (Z = -2.324, P = 0.020). Overall, the RPE proved to be a useful tool for most individuals and could be used in individualised exercise prescription, although women may overestimate, and regular exercisers may underestimate exertion.