Born in Grande Prairie, Alberta, Wharton attended the University of Alberta and the University of Calgary. He was a student of Rudy Wiebe and Greg Hollingshead. His first novel began as his M.A. thesis, under the supervision of Kristjana Gunnars. He worked on his PhD at Calgary with Aritha van Herk. Wharton is currently a professor of writing and English at the University of Alberta in Edmonton, and head of the creative writing department.

Wharton's first book, Icefields (1995), was awarded the “Best First Book” in the Canada and Caribbean division of the Commonwealth Writers Prize, the Writers Guild of Alberta “Best First Book Award”, and the Banff Book Festival grand prize.

His second book, Salamander (2002), won the Georges Bugnet Award for Fiction and was short-listed for the Governor General's Award for Fiction and the Grant MacEwan Author's Award (2002). It was also a finalist for the Rogers Writers' Trust Fiction Prize.

The Logogryph was short listed for the International IMPAC Dublin Literary Award.

Wharton's Icefields was a finalist in the Canada Reads competition in early 2008.

He is currently working on a three-volume fantasy novel for younger readers.