While still part of the Cascades, Pelican Butte is disconnected from the main axis, forming above faults along the eastern border of the range.

These eruptive episodes built a summit cone with tuff breccia and lapilli, later covered by lava flows before it was eroded.

Ancestral Native American groups related to the Klamath and Takelma people first hunted and gathered huckleberries in the area thousands of years ago.

The Sky Lakes Wilderness area eventually became a popular location for white settlers to hunt, trap beaver and marten, and graze stock.

A fire lookout tower is present on the summit of the volcano and is maintained by the United States Forest Service.

[11] Pelican Butte has a large volume at 4.8 cubic miles (20 km3), making it one of the bigger Quaternary volcanoes in the region of Crater Lake and Mount Shasta.

[14] Close to the summit, endangered western white pine trees support populations of Clark's nutcrackers and gray jays.

[20] The continuity of the Quaternary Cascade arc is interrupted at several points, including a potential gap between Pelican Butte and the Big Bunchgrass shield volcano to the north.

For the lower volcano, thick lava flows followed existing channels and formed glassy deposits with phenocrysts including plagioclase, augite, hypersthene, and olivine.

With a finer grain and vesicular texture, the lava has phenocrysts of white plagioclase with sodic labradorite as well as olivine, augite, and hypersthene.

[23] Vesicular lava flows are frequently observed near the summit of the volcano with white plagioclase phenocrysts made of sodic labradorite.

[11] In general, basaltic andesite deposits are 75–80% plagioclase, 8–10% clinopyroxene, and 8–10% orthopyroxene, with olivine ranging from 2–5%, typically occurring in an altered form as iddingsite.

These deposits are more aphyric (lacking any phenocrysts) and have a blue gray color with thin white streaks running subparallel to flows.

[13] Dated to between 60,000 and 12,000 years old, it produced basaltic andesite lava flows that have not been heavily eroded, but during Pleistocene glacial advance, ice streams on the volcano ate away at the cinder cone that formed Brown Mountain's summit.

Eruptive activity at Pelican Butte was mildly explosive, later switching to thinner flows with ʻaʻā and block lava.

It was also known by Native Americans as Mongina; the United States Coast and Geodetic Survey previously listed it under the name Lost Peak.

[3][29] Ancestral Native American groups related to the Klamath and Takelma people first hunted and gathered huckleberries in the area thousands of years ago.

Mountains in the Cascades sometimes served as the setting for the rite of passage vision quests among young Klamath Native Americans.

The United States Forest Service began building trails and fire lookouts during the early 20th century.

The peak of Pelican Butte offers a 180 degree view of the Cascades stretching from south of Crater Lake to Mount McLoughlin.

[33] The Pacific Crest Trail passes through the Sky Lakes wilderness area, running about 35 miles (56 km) in length.

[16][34] As of 2017[update], there were no plans to develop a ski area on the mountain according to an official representing the Fremont-Winema National Forest administration.