Kansas made the official announcement about a couple hours after the Owls beat Marshall, 41-24.
Reagan spent five years as offensive line coach and run-game coordinator at Kansas earlier in his career. He fills a vacancy in the Jayhawks' coaching staff created by the departure of offensive line coach Tim Grunhard, who chose to step down to spend more time with his family.
"When Tim told me his thoughts, I started searching for a replacement with the hopes of finding someone with Kansas ties capable of coordinating an offense," Kansas coach Charlie Weis said. "John not only coached at KU, but his kids still reside in Lawrence. He has a great reputation as an offensive line coach, but also has received accolades for coordinating the offense at Rice."
Weis revealed that Grunhard would be stepping down before the Jayhawks wrapped up a 3-9 season with a loss to rival Kansas State. Weis said at the time that he already had hired a replacement.
Weis also announced Saturday that linebackers coach Clint Bowen, who started calling defensive plays late in the season, will add the title of defensive coordinator. Weis said that Dave Campo, who has mostly been in charge of the defense, will remain as the assistant head coach.
"I like the way the defensive staff transitioned this past season from Dave to Clint," Weis said. "Therefore, Clint will now assume the title of defensive coordinator with Dave continuing to oversee the defense as the assistant head coach."
Reagan is considered one of the bright young offensive minds in college football.
After serving on Mark Mangino's staff at Kansas, he's spent the past four seasons at Rice -- the past three as offensive coordinator. Under his guidance, the Owls averaged more than 420 yards and 30 points this season, and boasted one of the nation's top run offenses.
In 2007, Reagan mentored Kansas offensive lineman Anthony Collins, an Outland Trophy finalist and fourth-round draft pick. He also coached All-Americans Jeff Spikes and Jeremiah Hatch.
"John immediately takes over for Tim and will hit the recruiting trail for offensive linemen," Weis said. "I would like to welcome John Reagan back to the Jayhawk family."