Most areas of the Appalachian Trail do not require fees or permits.
However, entrance or parking fees are collected at some national and state parks that the Trail passes through. Permits are required of backpackers in just a few locations. Some overnight sites, especially in New England, require fees.
See below for more details.
More information about regulations pertaining to camping and fires along the A.T. can be found here.
All overnight hikers, including thru-hikers, are encouraged to participate in a voluntary registration system, ATcamp.
Registering will help you avoid crowded areas and will help preserve the Appalachian Trail.