Myopia, or near-sightedness, is the most common refractive vision disorder and predisposes the eye to many blinding conditions in adulthood. Recent research has suggested that myopia is associated with increased endogenous melatonin production. Here we investigated the differences in melatonin circadian timing and output in young adult myopes and non-myopes (or emmetropes) as a pathogenesis for myopia. A total of 18 myopic (refractive error [mean ± standard deviation] -4.89 ± 2.16 dioptres) and 14 emmetropic participants (-0.09 ± 0.13 dioptres), aged 22.06 ± 2.35 years were recruited. Circadian timing was assessed using salivary dim light melatonin onset (DLMO), collected half-hourly for 7 h, beginning 5 h before and finishing 2 h after individual average sleep onset in a sleep laboratory. Total melatonin production was assessed via aMT6s levels from urine voids collected from 06:00 pm and until wake-up time the following morning. Objective measures of sleep timing were acquired a week prior to the sleep laboratory visit using an actigraphy device. Myopes (22:19 ± 1.8 h) exhibited a DLMO phase-delay of 1 hr 12 min compared with emmetropes (21:07 ± 1.4 h), p = 0.026, d = 0.73. Urinary aMT6s melatonin levels were significantly lower among myopes (29.17 ± 18.67) than emmetropes (42.51 ± 23.97, p = 0.04, d = 0.63). Myopes also had a significant delay in sleep onset, greater sleep onset latency, shorter sleep duration, and more evening-type diurnal preference than emmetropes (all p < 0.05). These findings suggest a potential association between circadian rhythms and myopia in humans.