Headaches from Charging Batteries?

If you have a friend who will do a blinded test for you, (a battery and charger in an opaque plastic container, plugged together or not plugged together) then you can figure out if the problem is real or psychosomatic. If real, there's various things you could try to mitigate it.

If psychosomatic, then good luck.

As others have mentioned, it is probably a high pitched noise. You may not be able to hear it, or maybe it is just on the edge and so very hard to judge volume. But if you can find a child they will likely be able to tell you if it is switched on or off just by listening. Or one of the many of us who can still hear poor quality LED lightbulbs and TV sets despite the years of hearing abuse. Google coil whine. Be careful with soundproofing, so you don't cause overheat and fire; better to get a replacement charger. Often another unit of the same brand won't have the problem, and you just have a substandard component. Other cases, such as some LED bulbs, you have entire product lines that whine.

Battery chargers often put out a very high frequency buzz that could be related but it may not be battery specific could just be electronics in general. Or just being indoors in general which happens to be where most electronics live.

Virtually all electronics these days use switched-mode power supplies/chargers.

I presume that your desktop computer has a metal case and typically desktop power supplies also have their own metal case. So if the desktop doesn't bother you, then it suggests that the double Faraday cage effect is working for you.

It would appear that you are either reacting to the super-audio whine of switched-mode chargers or possibly even the high frequency EMF radiation. Both sources are known to cause distress in some persons.

Personally, I sleep far better by not having any electronics in the bedroom and even switch-off power outlets near the bed. In the days of CRTs I used to be bothered by screen flicker. I could only tolerate Sun workstation monitors and some high-end Sony screens - all running at 75+Hz refresh rates.

Hard to assess. If the charger uses a high frequency switching power supply = you may be strangely sensitive? One easy solution is to place the charging battery in a metal box = a Faraday Shield or cage. This block radiated energy. The power cord must go through a gap n the lid, but 99% of the radiated energy will be blocked(depends on whatever gap you leave) - one assumes normal AC line radiation is not a problem as it has not happened before.

https://en.wikipedia.org/wiki/Faraday_cage

It seems highly unprobable because the reach of any radiation caused by the power supply would not extend far enough to fill a room. even though, it is extremely highly unlikely, it would more sense if you had headaches from cellular towers instead.

people are suggesting a blind test, I say, do a triple blind test.

ps. depending on the charger and the equipment I was able to hear it charging when I was young. but it is more likely to be because of how old equipments were and my family has a historic of hearing very high frequencies from almost any electrical equipment.

I would think it's something like coil whine. I often get annoyed by crappy chargers making high-pitched noises, and high pitches definitely have the propensity to cause headaches.

There is something called "EHS" and unfortunately there is lots of woo and pseudo-science around it, but also some legitimate anecdotal reports. Hopefully as another commenter has suggested you can do some double-blind testing to see if that's truly the cause.

Since you haven’t written how long it takes to set it I assume you are lying