Eight others were also indicted in the alleged scheme involving "straw purchasers" and "straw buyers" of houses, said FBI spokesman Mark White.
An alleged co-conspirator, realtor Lendell Beacham, of Desoto, was also arrested.
"It's been a long-term investigation," White said.
Federal prosecutors said the alleged scheme, from 2001 until 2005, involved 54 fraudulent loans totalling $20.5 million.
Among the others indicted were Michael Caldwell, 49, of Arlington, the former general manager of New Land National Title Inc. in Pantego, and Bryan Moorman, 67, of Mesquite, an appraiser.
The fraud involved inflated appraisals and false loan applications. In some cases, "straw buyers" and "straw purchasers" were paid between $10,000 and $20,000 to participate in the scheme, the FBI said.
Lockhart, the lead defendant in the case, used companies with names related to his former team, including "America's Team Mortgage" and "Cowboys Realty," said Kathy Colvin, a spokeswoman for the U.S. Attorney's office in Dallas.
Lockhart and Beacham were scheduled to appear before a federal magistrate at 1 p.m. If convicted, they could face up to 30 years in prison and a $1 million fine.
Lockhart joined the Cowboys in 1984 and played for seven seasons, earning the nickname "Mean Gene, the hitting machine" for his hard hits. He was born in Crockett and attended the University of Houston before being drafted by Tom Landry and the Cowboys in the 1984 draft.
Lockhart was traded to the New England Patriots in 1991, where he played his final two years of professional football.