Of Huguenot descent, he was born in Liberty County, Georgia, to Louis Le Conte, patriarch of the noted LeConte family, and Ann Quarterman.

[2] (In 1844 he travelled with his cousin John Lawrence LeConte for over one thousand miles along the Upper Mississippi River in a birchbark canoe.

[3]) After practising for three or four years in Macon, Georgia, he entered Harvard University and studied natural history under Louis Agassiz.

Joseph was appointed the first professor of geology and natural history and botany at the university, a post which he held until his death.

[2] As separate works he published Elements of Geology (1878, 5th edition 1889); Religion and Science (1874); and Evolution and its Relation to Religious Thought (1888).

He died of a heart attack in Yosemite Valley, California, on July 6, 1901, right before the Sierra Club's first High Trip.

[16] Leconte, along with other founders of the Sierra Club were advocates of white supremacy and supporters of the eugenics movement in the United States.

[17][18] The elementary school at 2241 Russell Street in Berkeley was named for Joseph LeConte from 1892 until 2018,[19] when it was renamed due to concerns regarding his views on race.