Central California boasts one of the PCT's most remote and beautiful sections - the Sierra Nevada. Spanning 400 miles (800 trail miles), the Sierra Nevada includes the longest wilderness, highest mountain, and deepest Canyon in the lower 48 states. For long-distance hikers and riders the region is a pleasure and a challenge. Elevations range from 8,000 to 13,200 feet and for 200 miles the trail doesn't cross a road.

Starting from this section's lowest point at Walker Pass (elev. 5,246'), the trail enters a roadless and wildly scenic realm, being met only occasionally by a dead-end road from the east. It hugs the relatively dry crest through the Chimney Peak Wilderness before reaching and crossing the South Fork of the Kern River near Kennedy Meadows. The route alternates between expansive meadows and conifer forests, then embarks on a 3,300' ascent and traverse to Cottonwood Pass.

In Sequoia National Park, the popular John Muir Trail descends from nearby Mt. Whitney (elev. 14,494') to join the PCT. The trails share the same tread for most of the way to Highway 120 in Yosemite National Park's lush Tuolumne Meadows (elev. 8,690'). Along this mostly wilderness stretch, the route repeatedly descends deep canyons only to ascend to high saddles. The PCT crosses eight named passes above 11,000' in this section, the first being Forester Pass (elev. 13,180'), the highest point on the entire trail. After crossing Highway 108 at Sonora Pass (elev. 9,620'), the altitude changes diminish in amplitude, and the trail soon begins a generally subalpine, relatively level traverse that stays close to the Sierra crest until this section ends at Interstate 80 (elev. 7200'). There is some volcanic rock south of Yosemite, but notable amounts are encountered from Sonora Pass to Echo Summit at Highway 50, and again near this section's end north of the Granite Chief Wilderness.

Animals in this section include marmot, coyote, deer, and black bear, the latter too often enjoying a meal of dehydrated food and granola bars left unguarded. Additional challenges in this section include icy high mountain passes (ice axes and knowledge of self-arrest are highly recommended) and snowmelt-swollen streams. During an average snow year, the Central California PCT becomes generally passable in mid-June for hikers and riders starting at Kennedy Meadows (often called the "gateway" to the Sierra Nevada). After mid-September, early winter storms bring fresh snow to the higher elevations.