Answer: A: The Pencil must make physical contact with the iPad. There must be no material between the Pencil and the iPad; if your case does not allow direct contact, the case is unsuitable - and will inhibit charging of the Apple Pencil.
Can I use Apple Pencil with a case?
Answer: A: It is neither a problem with your Apple Pencil or iPad. It is a problem with your case. You cannot use a case that cover iPad's right side as this will prevent Apple Pencil from charging.
Can you use Apple Pencil with Otterbox case?
While not marketed as waterproof, the case also incorporates port covers to block liquids and debris. Otterbox added that the product shouldn't interfere with the Apple Pencil, and in fact includes a holder for the stylus in its detachable stand/front shield.