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The transduction of light energy at the retina goes on to affect a range of non-image forming processes, most notably circadian photoentrainment, mood, and the pupillary light reflex. Our lab has previously demonstrated that retinal phototransduction can also modulate an animal’s breathing. However, it remains unknown how the timing of a light stimulus alters phototransduction and resulting behavior. Here, we investigate how unpredictable light stimuli affect respiratory frequency and tidal volume in mice. Male C57BL/6J mice (n = 8) were maintained on a 12:12 light–dark cycle, and breathing was assessed using whole-body plethysmography. All light stimuli were presented during the animals’ dark phase, either 1 hour after lights off (“early” dark phase, ZT13 to ZT16) or 5 hours after lights off (“late” dark phase, ZT17 to ZT20). As supported by our prior research, early light stimuli immediately suppressed breathing and, later, led to an increase in breathing after stimuli offset. However, late dark phase stimuli failed to affect respiration, even when spectral composition of the light was modified. These data demonstrate that the timing of light has differential effects on breathing. These data may implicate time-dependent differences in phototransduction and/or time-dependent differences in signal processing which go on to affect fundamental physiological processes.