Times have changed. Not that long ago thru-hikers only needed two permits during the entire 2,200-mile trek. Both were free and obtained at self-serve trailside kiosks. The purpose of the permits was to collect statistical data about how many people were using the trail so that the National Park Service could report this information to lawmakers and secure funding necessary to maintain the trail.
Today, the growing trend of user fees that is creeping through all of our public lands has made it onto the AT.
Great Smoky Mountains National Park (Tennessee/North Carolina)
The Park Service defines a thru-hiker as someone who begins and ends their hike at least 50 miles outside the park and only travels on the AT while in the park. Thru-hikers are required to have an AT thru-hiker's permit.
For northbound thru-hikers this means going online the day before you leave for the trail, paying the fee, and printing out the permit. The average hiker (who does not get injured early on and is forced to stay at Neel's Gap to recover) will reach Fontana Dam (the northbound entrance to the park) before 30 days. It is best to wait to get the permit until the last minute before you leave, that way you have wiggle room in case you are injured or some other unforeseen event slows you down.
Shenandoah National Park
Hikers pick up permits at trail-side, self-serve kiosks at entrances to the park. They are free, do not need to be requested in advance, and do not require approval from a park official. There is no charge for hikers entering the park via the Appalachian Trail.
Green Mountain National Forest (Vermont)
There are fees to camp at some high-use campsites. A Green Mountain Club caretaker may be present at other sites, but a fee is not charged. No additional permits or reservations are required.
The White Mountains (New Hampshire)
Baxter State Park (Maine)
Thru-hikers on the AT (anyone hiking 100 miles before entering the park) may stay at The Birches campground without a reservation, but must pay a camping fee. If the site is full, thru-hikers must wait for space to become available.