Judge Robert N. Chatigny has faced Republican criticism for his handling of a death penalty case.
Obama first nominated him in February for a seat on the 2nd U.S. Circuit Court of Appeals in New York.
A White House official said on Thursday that Chatigny asked to withdraw his name. The official spoke on condition of anonymity in order to discuss the nominations process.
Chatigny said in a statement released on Thursday that the nomination was an honor.
He was criticized by conservatives for threatening the license of a defense attorney who helped serial killer Michael Ross to expedite his death sentence in 2005. A review panel cleared the judge of any wrongdoing.