The Grand Canyon Railway starts at its ex-Santa Fe depot on the north side of the line in Williams (MP 0.0), where there is a yard, next to the Santa Fe line to Phoenix. The line is at an altitude between 6800-7000 ft. at the end points, descending to around 5200 ft. in between, with grades at both ends but generally flat, if undulating, in the middle. The lineside vegetation starts out as pine trees, then becomes scrub with scattered bushes as the line drops down from Williams, and later reverts to pine trees as the line climbs up again approaching the Grand Canyon National Park.
The single track, Track Warrant Control, line heads east from the depot, with speed limit 10 mph, and almost immediately turns north past the GCR carriage depot, under Interstate 40, past the GCR locomotive depot, and under the Santa Fe main line west to Seligman.
There is a long, low, trestle at MP 4, still among the trees, followed by Pitt (MP 7.8), where the speed limit is 35 mph and there was once a lumber spur on the east side of the line. By Red Lake (MP 9.0), where the speed limit reaches the line's maximum of 40 mph, the trees have been left behind to the south. The line continues north, with occasional curves, past Bly (MP 15.8), Quivero (MP 20.5), and Valle (MP 29.0), where the line heads curvily north-northwest. Crossing Miller’s Wash, the San Francisco Mountains are clearly visible to the east.
The line turns north again, past the 1,300 ft. siding at Willaha (MP 37.7), Woodin (MP 43.8), Anita (MP 44.9), where a spur once headed east to the Anita Mine, and the line turns curvily north-northeast. The big climb on the line is Apex Hill, with grades between 2.2% and 3.5%. There is a big s-curve on the hill at MP48, where there is a 3% grade, Hopi (MP 50.0), and the summit is reached at Apex (MP 52.0), where the speed limit is 30 mph and there were once many lumber spurs off to the east, after which the line turns north-northwest, makes a counter-clockwise horseshoe back to the south-southwest and a clockwise horseshoe to the north-northwest again as it drops into Coconino Canyon, past.Coconino (MP 57.2), where the speed limit is 25 mph, as the line turns northeast, climbing out again.
The line approaches the National Park on a 3% upgrade, surrounded by tall trees, almost 64 miles from Williams, turning due east, past a wye on the south side of the line used for turning the trains, to the Grand Canyon depot (MP 63.7), where the speed limit is again 10 mph and there is a small yard, about 200 yards from the canyon rim, immediately south of El Tovar, the former Fred Harvey hotel at the canyon.