About this permit
The John Muir Trail runs 211 miles from Yosemite Valley to Mount Whitney, and for most of that length it overlaps the Pacific Crest Trail. If you hike it as a continuous trip, NPS says you need exactly one wilderness permit, a Yosemite one, for the whole thing.
What you are actually competing for is a trailhead entry date. Yosemite issues permits to a limited number of people each day per trailhead, based on entry date and entry point, and it measures those quotas per person rather than per permit. On top of that sits the Donohue Pass exit quota, introduced in 2015: the park issues permits valid for exiting Yosemite over Donohue Pass for up to 45 people per day, 15 of them from Happy Isles to Past LYV and 30 from Lyell Canyon. Those are the only two trailheads that reach the full JMT beyond the park.
Cancellations are the way in all season. Yosemite releases cancelled quota the moment someone cancels, holds forty percent of every trailhead's quota until seven days before the entry date, and puts leftover lottery places on first-come, first-served sale the Friday after each application week. A cancellation alert on the JMT trailheads catches all three. The weekly lottery covers the other sixty percent, 24 weeks ahead: apply Sunday 12:01 am to Saturday 11:59 pm, results the following Monday by 5 pm Pacific, payment by Thursday 11:59 pm. One application per group, and NPS defines a group as anyone who may be planning to hike together, cancelling duplicates without refund.
A permit is $10 to enter the lottery plus $5 per person when you confirm, and none of it is refundable.
The route
The John Muir Trail runs 211 miles from Yosemite Valley to Mount Whitney, and it overlaps the Pacific Crest Trail for most of its length. Inside Yosemite the trail's high point is Donohue Pass at 11,056 feet, on the park's southern border, which is exactly where the quota bites.
Only two trailheads give access to the full JMT beyond Yosemite: Happy Isles to Past LYV (Donohue Pass eligible) and Lyell Canyon (Donohue Pass eligible). Of the 45 people a day allowed to exit over Donohue Pass, 15 come from Happy Isles and 30 from Lyell Canyon. If you start at Happy Isles, your first night cannot be in Little Yosemite Valley.
Everything downstream of Yosemite is covered by that one permit. Bear canisters are required throughout the park, food hanging is not permitted anywhere in Yosemite, and there are no exceptions for through-hikers. Resupply goes by General Delivery to the post offices in Yosemite Valley and Tuolumne Meadows. Ranger stations do not accept food packages.
Why it matters
This is not a permit for a trail. It is a Yosemite wilderness entry permit for a specific trailhead on a specific date, which happens to be the thing that unlocks the John Muir Trail. NPS puts it plainly: if you hike the JMT as a continuous hike you only need one wilderness permit from Yosemite for the entire trip: no Whitney stamp, no permits from the forests and parks in between. The exit quota is what decides it. Yosemite limits hikers exiting the wilderness over Donohue Pass to 45 per day, and only two trailheads are Donohue Pass eligible.
