The McCloud River Railroad is operated by means of DTC “Blocks”. It heads north from the "yard" at Mount Shasta (MP 15.2), in Yard Limits with speed limit 15 mph for passenger trains and 10 mph for freight trains, turning northeast and crossing the road at an angle. The line curves around in a clockwise direction, first to the east (MP 15), across another grade crossing, entering the Mt. Shasta Block at MP 14.6, and starting up a steep grade, and then south (MP 14). The line then curves counter-clockwise, to the northeast, still climbing steeply, before curving clockwise back to the southeast, through Howard (MP 12.1) and the dense evergreen forest, and then east, southeast, south, east, and south again, climbing all the way on a 4% grade through Big Canyon and all the way to the summit at Pierce. A gradual curve to the southeast is punctuated by a dirt road grade crossing, followed by a curve south (MP 12), then an anticlockwise curve through another dirt road grade crossing all the way around to the northeast and then back clockwise to the south. The line is now a long way above the valley floor below and to the south. A curve back east at MP 11 is followed by another one south and even southwest, past Big Canon (MP 10.0). The line then curves along the south slope of Mount Shasta, heading generally east, past the 1,717 ft. siding Pierce (MP 7.2), where the Mt. Shasta Block ends and the Pierce Block starts, but curving back and forth to follow the contour line the whole way.
The line from McCloud comes up from the south and joins with the one from the west at into the long (2,861 ft.) tail track that continues curving along the hillside at Signal Butte (MP 5.1). There is a grade crossing along the tail track, along with the remains of a one-time turntable pit on the south side of the line. The line to McCloud from the tail track turns south, heading steadily downhill, and then curves back and forth between extremes of west and east, all generally heading south, and then turns generally east, passing through Hooper (MP 2.3) and curving back and forth between extremes of northeast and southeast, with Mount Shasta’s south face always in view to the north, crossing a dirt road, reaching Yard limits and turning southward. Another grade crossing leads to the west apex of the wye with the line eastward, at North McCloud (MP 1.0), where the Pierce Block ends and Yard Limits start, passing to the west of the shops in the middle of the wye, and continuing past the south apex of the wye into the station at McCloud (MP 0.0), where there is a platform on the east side of the line, next to a greensward alongside the town’s main street, and carriage sidings on the west side.