Nuffer started as a part-time magistrate in 1995 and moved to full-time in 2003. Before that, he had a lengthy career as a partner in a law firm where he focused on civil litigation and real estate development.
Obama nominated Nuffer at the same time he nominated Thomas Owen Rice to become a district judge in Washington state.
"I am honored to nominate these distinguished individuals to serve," Obama said in a statement. "They have both demonstrated an unwavering commitment to justice throughout their careers."
If confirmed, Nuffer would take the spot vacated by Judge Dale Kimball, who moved to senior status taking a lighter case load starting in 2009.
Utah Sens. Orrin Hatch and Mike Lee, both members of the Judiciary Committee, expressed support for Nuffer's nomination.
"Judge Nuffer is an experienced, highly regarded judge who will serve the people of Utah well in his new role," said Lee.
Hatch said: "Judge Nuffer's integrity, training and legal experience make him well-qualified for the position."
Utah still has one vacancy on the district court.