Can you take an Apple Pencil with your iPad on an airplane? How do you take it through secuirty?

I’ve never experienced any issues with carrying an Apple pencil on commercial flights - or with airport security in general.

While my own Pencils are often located in the associated slot of the STM Dux Case that houses the iPad Pro 10.5”, or the Otterbox Symmetry 360 Case of the iPad Pro 12.9”, I’ve also carried the Pencil along with other pens in a jacket pocket.

As Muguy said, put it in your carry on. TSA rules change all the time but last time I flew large electronics did need to be scanned on their own (not remaining in the bag) but I’d be willing to bet that thousands of ipads fly every day.

Sure. You're probably planning to use it so leave it in your carry on bag.