This experimental study examined the influence of smartphones on affective responses and time perception in exercise. Twenty-four physically active participants (16 females, 8 males; Mage = 24.40, SD = 4.35) completed randomised conditions alternating between hard intensity cycling and seated rest whilst their smartphone was: a) used to view videos; b) present but not viewed; or c) out of sight. In each condition, participants produced a target amount of time (i.e., 37s) during the trial and estimated the trial’s duration upon completion (i.e., 330s). Participants’ feeling state, perceived exertion, and heart rate were recorded at each measurement of time perception during and following each trial. One-sample t-tests and repeated measures ANOVAs indicated that smartphones significantly affected participants’ perception of time during and following intervals of cycling and rest. Participants perceived more time had passed than chronometric time during cycling; this effect was most significant when viewing their smartphone. Participants estimated that the duration of each trial was less than actual chronometric time, although they were more accurate when they viewed their smartphone during the trial. Participants reported the greatest positive affect when viewing their smartphone, although it was not associated with time estimation accuracy. These findings highlight that highly trained exercisers overestimate the passage of time during physical activity, yet upon completion, they perceive they exercised for a shorter amount of time than reality. Smartphones can distort time perception and influence affective responses to exercise; this may have implications for the evaluation of physical activity, intentions to exercise, and health behaviours.