The 63-year-old has held the position since June 2004 and will be replaced by Bayer AG communications manager Michael Schade as of July 1, 2013.
"It's a good time to bow out," explained Holzhäuser. "Bayer 04's future is bright. We've got a great team on and off the pitch. In qualifying for the UEFA Champions League with two games to go, we've surpassed our expectations for the season. After 15 years in the job, it's the ideal time to take a step back from the operational side of things."
Holzhäuser, who will join the board of directors in the autumn, became a member of the club in 1998. He went on to take up the role of vice president and then president of the football league association in 2004 and 2007 respectively.