Human time perception is malleable and subject to many biases. For example, it has repeatedly been shown that stimuli that are physically intense or that are unexpected seem to last longer. Two competing hypotheses have been proposed to account for such biases: One states that these temporal illusions are the result of increased levels of arousal that speeds up neural clock dynamics, whereas the alternative “magnitude coding” account states that the magnitude of sensory responses causally modulates perceived durations. Common experimental paradigms used to study temporal biases cannot dissociate between these accounts, as arousal and sensory magnitude covary and modulate each other. Here, we present two temporal discrimination experiments where two flashing stimuli demarcated the start and end of a to-be-timed interval. These stimuli could be either in the same or a different location, which led to different sensory responses because of neural repetition suppression. Crucially, changes and repetitions were fully predictable, which allowed us to explore effects of sensory response magnitude without changes in arousal or surprise. Intervals with changing markers were perceived as lasting longer than those with repeating markers. We measured EEG (Experiment 1) and pupil size (Experiment 2) and found that temporal perception was related to changes in ERPs (P2) and pupil constriction, both of which have been related to responses in the sensory cortex. Conversely, correlates of surprise and arousal (P3 amplitude and pupil dilation) were unaffected by stimulus repetitions and changes. These results demonstrate, for the first time, that sensory magnitude affects time perception even under constant levels of arousal.