Charpentier studied under Abraham Werner at the Mining Academy in his native city of Freiberg, where his father was also a professor. He worked as an engineer in the Silesian mines before being appointed director of the Bex salt mines in 1813.

He studied the problem of the widely scattered and impressively large erratic boulders and soon rejected the current theories of their origin. The theory that such boulders were meteorites was unlikely for they were identical in composition with other Alpine rocks. The flood theory, supported by Charles Lyell, supposed that they had been distributed by boulder-laden icebergs. However, this raised the problems of where the water had come from and where it had gone to.

Charpentier concluded that the agent responsible was glaciation and first presented his glacial theory publicly in Lucerne in 1835. He gained little support but did attract the attention of Louis Agassiz. In 1841 Charpentier published his results in his Essai sur les glaciers (Essay on Glaciers) but was anticipated by Agassiz's earlier publication, in 1840, of his Etudes sur les glaciers (Studies on Glaciers).