Why You Keep Waking Up at 3 AM (And What Melatonin Might Have to Do With It)

You fall asleep fine. You are doing the whole “good bedtime” thing. Then bam. Eyes open at 3:00 AM like your brain just punched a time clock. You check the dark. You check the silence. You check your pulse. And now you are wide awake, wondering if this is stress, hormones, blood sugar, or some mystical message from the universe.

Let’s talk about a less dramatic, more sciencey suspect: melatonin timing and how fast your body is burning through its night signal.

Melatonin is not a sleeping pill. It is a timing signal.

Melatonin is a hormone your brain releases at night to tell your body, “It is biological night now.” It helps coordinate your circadian rhythm, which is your internal 24 hour clock that influences sleep, temperature, hormones, and alertness. In sleep research, melatonin is often treated like a built in “clock marker” because its rise in the evening is a reliable sign that your body is shifting into night mode.¹ ²

Melatonin can also support sleepiness and sleep continuity, but its bigger job is keeping your body’s timing aligned.² When that timing is off, sleep can get choppy.

Your melatonin curve has a beginning, a middle, and an end

In many people, melatonin starts rising a few hours before habitual bedtime, stays elevated during the night, and then falls toward morning. In delayed sleep wake phase disorder (DSWPD), researchers have found melatonin timing and nighttime profiles can differ from controls, which lines up with the real world experience of “my body wants to sleep later than my life allows.”¹

You Were Never Called to Perform.

If hustle has replaced peace and performance has replaced purpose, this book will help you rebuild your work on righteousness, integrity, and obedience, without burnout.

Order Your Copy Today

Here is the part that matters for the 3 AM crowd: if your melatonin rise starts too late, peaks oddly, or drops sooner than your sleep window expects, sleep maintenance can suffer.¹

The “phase angle” is the sleep timing detail most people never hear about

There is a nerdy but important concept called the phase angle, which basically means the time relationship between when melatonin starts rising and when you try to sleep. When that relationship is “off,” sleep can become lighter and easier to break. Research looking at melatonin onset timing in people who report delayed sleep schedules highlights how relevant this timing relationship can be.³

And measuring this matters, because home versus lab testing can produce different melatonin onset estimates, which is a big deal if you are trying to understand whether your early waking is a circadian timing issue or something else.³

So why 3 AM specifically?

A lot of people experience wake ups in the later part of the night because that is when sleep naturally becomes lighter and your body starts drifting toward morning biology. If, on top of that, your melatonin signal is dipping earlier than your sleep window expects, you can get the classic pattern: you wake up, and your system is already sliding toward “day mode.”

We do have research examples where impaired or disrupted melatonin secretion shows up alongside fragmented sleep and frequent awakenings, including in circadian rhythm disorders.⁴ The takeaway is not “melatonin runs out at 3 AM for everyone.” The takeaway is “when the melatonin signal is mistimed or impaired, sleep continuity can take a hit.”¹ ⁴

Light is a melatonin disruptor, and your eyes are the gateway

Light exposure is one of the strongest regulators of your circadian clock. Short wavelength light (often described as blue light) can suppress melatonin and shift circadian timing.⁵

Even more interesting: people with delayed sleep wake phase disorder appear to have increased sensitivity to light, meaning the same light exposure can create a bigger circadian effect compared to controls.⁶ If your system is more light sensitive, late evening light or bright nighttime light might push your timing later and make the back half of the night more fragile.

Training schedules, screens, and “revenge bedtime” are not neutral

Real life behavior matters here.

• In young professional football players, melatonin secretion patterns and sleep quality were discussed in relation to training and match schedules, pointing to how lifestyle timing can interact with circadian rhythms and recovery.⁷
• In young adults, electronic media habits have been associated with sleep quality differences across circadian typology (your natural early bird versus night owl tendency).⁸

Translation: your biology is doing biology, but your calendar and your phone are also doing biology.

The “earlier bedtime” idea works best when it is paired with circadian strategy

A lot of people hear “go to bed earlier” and want to throw a pillow.

The research angle is more specific: when sleep timing is gradually shifted earlier and paired with appropriately timed light exposure, circadian rhythms can be phase advanced, meaning moved earlier.⁹ In other words, earlier bedtime is not just a moral virtue. It is a timing intervention, and it tends to work better when the rest of your light and schedule cues support it.

This also shows up in development research. Sleep wake rhythm maturation in the first year of life is tied to building stable patterns and consolidated sleep, which is basically the baby version of circadian alignment.¹⁰ And in toddlers, sleep timing patterns (like napping versus not napping) relate to differences in circadian timing.¹¹ Your clock has always cared about timing.

Where supplemental melatonin fits in the literature (and where it does not)

In studies, exogenous melatonin (melatonin taken from outside the body) has been used as a tool to shift circadian timing when given at specific times relative to melatonin onset.¹ ⁹ This is less about knocking someone out and more about nudging the internal clock.

There is also research on broader chronobiological approaches, including multimodal interventions that track melatonin rhythm changes alongside symptom changes in specific populations.²

Important coaching note: this is not a DIY dosing invitation. The timing details are the whole point, and different sleep problems can look the same on the surface.

What to do with all of this if you are the person staring at the ceiling at 3 AM

If you keep waking up around the same time, think in “clock language” as well as “stress language.” Ask: is my sleep window matched to my biology, or am I trying to sleep at a time when my circadian system is already drifting toward morning? Consider your evening and nighttime light environment, your screen habits, and whether your schedule is quietly training your clock to run later. And if you want to experiment, focus first on the boring fundamentals that actually move the needle: consistent sleep timing, morning light exposure, and dimmer evenings. The punchline is simple: **when your melatonin rhythm and your sleep schedule cooperate, staying asleep gets easier. When they fight, 3 AM wins.**¹ ⁶ ⁹

References

1. Micic, G., Lovato, N., Gradisar, M., Burgess, H., Ferguson, S., Kennaway, D., … & Lack, L. (2015). Nocturnal Melatonin Profiles in Patients with Delayed Sleep Wake Phase Disorder and Control Sleepers. Journal of Biological Rhythms, 30(5), 437 to 448.
2. Robillard, R., Carpenter, J., Feilds, K., Hermens, D., White, D., Naismith, S., … & Hickie, I. (2018). Parallel Changes in Mood and Melatonin Rhythm Following an Adjunctive Multimodal Chronobiological Intervention With Agomelatine in People With Depression. Frontiers in Psychiatry, 9.
3. Moderie, C., Maren, S., Paquet, J., & Dumont, M. (2019). Home versus laboratory assessments of melatonin production and melatonin onset in young adults complaining of a delayed sleep schedule. Journal of Sleep Research, 29(3).
4. Ferri, L., Filardi, M., Moresco, M., Pizza, F., Vandi, S., Antelmi, E., … & Plazzi, G. (2017). Non 24 Hour Sleep Wake Rhythm Disorder and Melatonin Secretion Impairment in a Patient With Pineal Cyst. Journal of Clinical Sleep Medicine, 13(11), 1355 to 1357.
5. Ostrin, L., Abbott, K., & Queener, H. (2017). Attenuation of short wavelengths alters sleep and the ipRGC pupil response. Ophthalmic and Physiological Optics, 37(4), 440 to 450.
6. Watson, L., Phillips, A., Hosken, I., McGlashan, E., Anderson, C., Lack, L., … & Cain, S. (2018). Increased sensitivity of the circadian system to light in delayed sleep wake phase disorder. The Journal of Physiology, 596(24), 6249 to 6261.
7. Almendros Ruiz, A., Conde Pipó, J., Aranda Martínez, P., Olivares, J., Acuña Castroviejo, D., Requena, B., … & Mariscal Arcas, M. (2025). Melatonin Secretion and Impacts of Training and Match Schedules on Sleep Quality, Recovery, and Circadian Rhythms in Young Professional Football Players. Biomolecules, 15(5), 700.
8. Gangwar, A., Rawat, A., Seth, S., & Verma, A. (2024). Association between sleep quality and habits of electronic media use among young adults with different circadian typology. Asian Journal of Medical Sciences, 15(5), 95 to 101.
9. Crowley, S., & Eastman, C. (2015). Phase advancing human circadian rhythms with morning bright light, afternoon melatonin, and gradually shifted sleep. Sleep Medicine, 16(2), 288 to 297.
10. Paavonen, E., Morales Muñoz, I., Pölkki, P., Paunio, T., Porkka Heiskanen, T., Kylliäinen, A., … & Saarenpää Heikkilä, O. (2019). Development of sleep wake rhythms during the first year of age. Journal of Sleep Research, 29(3).
11. Akacem, L., Simpkin, C., Carskadon, M., Wright, K., Jenni, O., Achermann, P., … & LeBourgeois, M. (2015). The Timing of the Circadian Clock and Sleep Differ between Napping and Non Napping Toddlers. PLOS ONE, 10(4), e0125181.