Former President Clinton nominated Sheila Widnall to lead the Air Force in 1993 under then Defense Secretary Les Aspin. Widnall served as service secretary for four years, leaving the post in 1997.
"I look forward to working with her to keep our Air Force the very best in the world and to keep faith with our extraordinary Air Force personnel and their families," the president added.
James, who is currently a senior executive at the U.S. defense firm SAIC, is set to replace former Air Force Secretary Michael Donley, who retired from the top service spot on June 21 after more than 30 years of service at the Pentagon and elsewhere.
Undersecretary of the Air Force Eric Fanning has been acting secretary since Donley's departure in June.
Defense Secretary Chuck Hagel had nothing but praise for James's nomination.
"Deborah is an outstanding leader with deep experience in the Department of Defense, the private sector, and non-profit organizations that support the men and women of our armed services," Hagel said in a statement.
James's nomination comes as the Air Force continues to cope with a raft of sexual abuse scandals that have rocked the services' ranks.
Nearly 32 Air Force trainers are under investigation for sexually assaulting more than 60 female service members at the Air Force's basic training facility at Lackland Air Force Base, Texas.
Of the 32 instructors, the Air Force had disciplined eight for sexual misconduct and deferred court martial against nine.
In May, the lieutenant colonel in charge of the Air Force’s sexual assault prevention and response branch was arrested in Arlington, Va., on suspicion of sexual battery.
Air Force Lt. Col. Jeff Krusinski, the officer in charge of the service's sexual assault prevention and response branch, was arrested on suspicion of sexual battery.
Krusinski was fired from his position at the service's sexual assault prevention and response branch, after he was charged with sexual battery in Arlington County.