Beaty, 44, had two stints as an assistant coach in Lawrence, Kansas, coaching the Jayhawks' wide receivers from 2008 to '09 before returning for a stint as the co-offensive coordinator and receivers coach in 2011.
The school fired Charlie Weis on Sept. 28, a day after a 23-0 loss to Texas. Weis was in his third season at the school and went 6-22 in his time leading the Jayhawks. Defensive coordinator Clint Bowen served as the interim head coach for the final eight games of the season for the 3-9 Jayhawks.
Bowen will remain on the Jayhawks' staff as defensive coordinator, Beaty announced.
"I am very excited to be back at Kansas," Beaty said in a statement. "I am especially excited that Clint Bowen has agreed to stay on as assistant head coach and defensive coordinator. Clint will be a huge part of our success going forward and I am fortunate to have him on my staff."
The school will formally introduce Beaty at a news conference at 9:30 a.m. CT Monday.
Beaty spent the past three seasons in College Station, Texas, as the Aggies' receivers coach and added recruiting coordinator to his title in 2013. He oversaw the development of Mike Evans, the No. 7 overall pick in the 2014 NFL draft who is enjoying a standout rookie season with the Tampa Bay Buccaneers and was an All-American in 2013 at Texas A&M.
Known as an ace recruiter, Beaty oversaw the Aggies' recruiting efforts in the talent-rich Dallas-Fort Worth metroplex, where he has roots as a high school coach. Beaty coached at four metroplex-area high schools from 1994 to 2005 before joining Todd Graham's staff at Rice in 2006 as the receivers coach. Beaty spent two seasons with the Owls before making his first move to Kansas.
The Jayhawks have struggled mightily in recent years, finishing ninth in the Big 12 this season and going 12-48 since the start of the 2010 season. They're 3-41 in Big 12 play in the past five seasons. The last time Kansas was over .500 and went to a bowl was 2008, which was Beaty's first season as an assistant in Lawrence under then-head coach Mark Mangino.
Beaty quickly emerged as one of the Big 12's top recruiters in his first season at Kansas, landing six recruits in the 2009 class and being named one of the top recruiters in the conference by Rivals.com that season. His roots in Texas will be key for the Jayhawks, who have long recruited the fertile state.
Under Beaty's watch, former Kansas receiver Dezmon Briscoe set the single-season school record for receiving yards (1,407) in 2008 and Kerry Meier became the first and only Jayhawks receiver to catch 100 passes in a season, hauling in 102 in 2009.
"David Beaty is well-respected in the football community and brings to KU great vision, passion and energy," Kansas athletic director Sheahon Zenger said in a statement. "He has a bright football mind and is known as one of the best recruiters in the nation."
This will be the first collegiate head coaching job for Beaty, a native of Garland, Texas. He spent his college playing career at Lindenwood University in St. Charles, Missouri, where he was a four-year starter for the then-NAIA program in the early 1990s.