The standard and most popular Philmont program is the trek. A typical Philmont trek lasts 10 days and covers anywhere from 50 to 100 miles of trail. A group of Scouts on a trek is called a crew; most crews are assembled by troops, Venturing crews, or local councils, and consist of people from the same area. A crew consists of seven to twelve people (usually ten or more), with two to four adult leaders and a crew leader. A contingent consists of one or more crews from the same council, traveling together. Around 360 trekkers arrive at base camp every day of the season.

A typical crew's experience is as follows:

The crew arrives in Base camp, checks in at the Welcome Center, and meets its ranger, a trained staff member from the Ranger Department. He or she assists them in the various registration ("processing") procedures, which consist of verifying their itinerary with Logistics and checking out gear, such as a dining fly, bear ropes, bear bags, and water purification tablets, from the Services building.

The dining fly is a 12-foot-square water-retardant blue tarp with two collapsible aluminum poles, which may optionally be replaced by trekking poles to save weight. Its purpose, quite contrary to its name, is to serve as a rain cover for the crew's backpacks. It is designed to be set up as an A-frame (see tent), with two opposite sides staked down, the middle supported by the poles and a ridgeline, and the ends open. Many crews experiment with the use of trees, hiking poles, and other devices to obtain a roomier configuration so that it can be used for crew activities such as games, and to increase its utility as a rain shelter or actual dining fly.

If crew members have not brought tents of their own, they may also check out Philmont's tents, known always as "Philtents". Philtents are two-man blue A-frames which measure five feet wide by seven feet long, are supported by two poles at the front and one at the back (no ridgepole), and come with a rain fly. They are more difficult to set up than conventional dome tents, but very easy to break down. They are reputedly bulky, but in fact are not significantly heavier than most ordinary dome tents.

A crew also receives several days' worth of Philmont trail food, packaged in bags which feed two people each; the exact quantity depends on the crew's itinerary and the day on which it is scheduled to reach the next commissary. Philmont also provides optional cooking supplies.

The crew spends its first night in Trailbound Tent City, where it has access to showerhouses and flush toilets. The trekkers sleep in tan canvas tents, each with a concrete foundation and two cots. The next morning, they eat breakfast at the dining hall and board a bus to one of the ranch's several trailheads, called "turnarounds" because they consist of a loop in the road for the bus to turn around. The crew and its ranger are now alone.

The ranger verifies the trekkers' general backpacking knowledge, and teaches them specific Philmont procedures, such as bear procedure and latrine usage. Rangers stay with their crews for two days, and depart on the morning of the third day on the trail. In the next eight days the crew will hike through the Philmont wilderness, staying at various Staffed camps and unstaffed "Trail camps" scattered about the Ranch. On the final day, the crew returns to Base Camp, sometimes by bus from a turnaround, but more popularly by climbing over the Tooth of Time and hiking directly into Base Camp from the rear. During the final day at Base Camp, the crew cleans up, returns various Philmont-issued supplies, including cookware and tents, and attends the closing campfire.