Apple Pencil not working and battery is always at 3%

Yup,

Lotus Pilot is correct.

Your Pencil battery may have failed and your Pencil may be dead, again.

Sorry.

You cannot store and/or NOT use Pencils for any prolonged period of time and NOT keep them charged up to some level.

If your Pencil/s sat around unused or unopened and not kept always charged up for more than a few weeks, or so, OR

EVEN LONGER, then the battery in your Pencil may have failed and is dead and you will have to purchase another

brand new Pencil or get, if still under warranty, a free replacement Pencil from Apple.

Sorry.

And it looks like some things about the Pencil have NOT changed in the new version 2 model, either.

Due to the “always on and active/standby” nature of the Pencil and, also, due to its very tiny rechargeable Li-

ion battery ( smaller than the eraser head on a REAL wooden pencil ), the Pencil needs to be constantly charged up to some significant charge level ALL THE TIME, even when not using the Pencil for prolonged periods of time.

The Pencil needs to be kept charged to a minimum of 5-10%, OR GREATER, all the time.

If the Pencil battery is allowed to drain down to 0% and allowed to stay in that flat condition for more than a few weeks, or so, OR EVEN LONGER, that very tiny little Li-ion battery is too small to keep at a 0% state for a long period of time and it will fail and the Pencil will be dead and you may have to “pop” for another $99/$129 Pencil, once again!

Apple only has a one-year warranty on any Apple accessory items.

You need to keep your Pencil charged all the time, even if it is only to 10%-15% charge. It must keep some charge level in that tiny Lithium-ion battery at all times!

One last ditch thing you can try is to plug the Pencil's Lightning connector into the iPad.

Then, try a simple hard reset of your iPad by holding down both the Home and sleep/wake buttons simultaneously until your iPad goes to black and restarts with Apple logo, then release the buttons.

OR

Put your Pencil 2 atop the magnetic charging edge of your iPad.

Then, try the new hard reset procedure for the 2018/2020 iPad Pro/iPad Air 4 models without a Home button.

1. Press and release the volume UP button.

2. Then immediately press and release the volume DOWN button.

3. Then, press and hold the Power button at the top. You will see the Slide to Power off button, but keep on holding down the Power button until you see the Apple logo, then let it go.

Once you have performed all the steps, wait for a few seconds and your iPad Pro will boot up completely to the iPad Pro’s Lock screen.

See if the Pencil starts charging then, when it reaches a sufficient charge, like over 15%, or so, or more, disconnect the Pencil and reconnect it to see if it Bluetooth pairs.

If it does pair, try using it.

If still no joy, your Pencil is definitely dead.

Sorry and Best of Luck to You!

Your Apple Pencil is exhibiting symptoms of a dead battery - that will not accept or hold any charge.

The tiny internal Li-ion battery is susceptible to permanent/irreversible damage through being left discharged for long periods. Even some “new” pencils can exhibit signs of failure out-of-the-box if they are “old stock”.

It is essential that if you have an Apple Pencil that you charge it regularly - whether used or not - so as to protect the battery from deep-discharge. Do not allow a pencil to remain in low-charge state for any period of time - as the internal battery will fail, rendering the Pencil useless. Setting aside an unused Pencil, for extended periods, is a recipe for premature death of the Pencil battery.

If the Pencil Battery has failed, the only remedy is to replace the Pencil. If the battery has failed and your pencil is within its one-year warranty, you should look to having it replaced by your retailer or at an Apple Store.