Apple pencil not charging properly

As described, your Pencil still works - but if failing to fully or consistently charge. The tiny Pencil battery may be failing - perhaps nearing the end of its usable service life.

Unless you have access to another iPad, where you can test and attempt to replicate the behaviour (in so doing demonstrating that the issue lies with the Pencil - and not the iPad), you might be best advised to visit the Genius Bar at your local Apple Store or Apple Authorised Service Provider (AASP) - where the technicians will be able to test and assess your iPad and the Pencil:

Genius Bar Reservation and Apple Support Options - Apple

Be aware that if your Pencil has been set-aside for an extended period, unused and uncharged, the Pencil battery may now be irretrievably damaged through deep discharge. In common with all Li-ion batteries, they must always have some level of 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. A second generation Pencil should be docked with the host iPad whenever the Pencil is not being actively used - as doing so will optimally charge and protect the battery from damage.

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.