Once the Bridger Trail reached Badwater Creek, the trail headed north to avoid the impassable Wind River Canyon and continued up Bridger Creek and over the Bridger Mountains near present-day Lost Cabin, Wyoming. At the summit of the divide, it crossed over to the eastern or south fork of Kirby Creek, which it descended to the Bighorn River. Bridger's train crossed the Bighorn River using a large raft or ferry built from trees felled along the river. The ferry was buried so it could be used by the trains following Bridger.

The trail continued along the west side of the Bighorn River, usually within a mile or less from the river until reaching the mouth of Nowood Creek. At this point, the trail left the Bighorn River and proceeded northwest to the Greybull River.

After crossing the Greybull, the trail continued west along the north side of the river to the vicinity of the big bend in the river, at which point it proceeded north until it reached the Shoshone River.

The trail crossed the Shoshone and continued northwest following Sage Creek, exiting Wyoming virtually on the Park/Big Horn County line. The trail continued north until it reached Clarks Fork of the Yellowstone River near present-day Bridger, Montana. The trail crossed Sage Creek, heading northwest approximately three miles to Bridger Canyon and the headwaters of Bridger Creek (shown on the General Land Office plat as the Big Horn Basin & Bridger Road). The trail continued due west along the north side of Bridger Creek and then left Bridger Creek, heading due north to the crossing of Clarks Fork of the Yellowstone River, southeast of present-day Bridger, Montana.

In 1864 the Bozeman Trail merged with the Bridger Trail where it first crossed Rock Creek, approximately one mile east of present-day Joliet. From this point on, except for minor variations, the combined trail followed Bridger's route to Virginia City.

The trail continued northwest across Rosebud Creek and the Stillwater River near Absarokee, Montana, then west to Bridger Creek and down that creek to the Yellowstone River. The trail continued west along the south side of the Yellowstone, crossed Boulder River near Big Timber, Montana, and continued along the Yellowstone for about sixteen miles to the crossing near Hunter Hot Springs and present-day Springvale, Montana, approximately seven miles east of the Shields River.

A ferry was built to transport the wagons across the Yellowstone. By July 4, the first three trains were camped on the south side of the Yellowstone River. Stanfield had reached the river about noon on the fourth, and "some of us commenced ferrying and other forded it. It is a beautiful river near a quarter mile wide a very strong current clear as crystal very good water to drink and we forded it about 5 and one half feet deep we crossed over without any serious accident and camped on the evening of the 4th on the banks of the Yellow Stone." Hedges also arrived on July 4, and his crossing of the river was uneventful as well. "Waited till Jacob's train passed . . . pushed on to ferry. . . . went over on boat. . . . We are up with Bridger & all. . . . Ferry charge $2.50."

Bridger's trail kept west along the north side of the Yellowstone, then proceeded north up the Shields River, west up Brackett's Creek and over the southern end of the Bridger Mountains, then down Bridger Creek to the Gallatin River west of present-day Bozeman, Montana. John Jacobs took a few wagons over what is now Bozeman Pass to the Gallatin River.

Well-rutted roads led from the Gallatin River to the Madison River, and members of the various trains headed at will south up the Madison to their destination of Virginia City.