Helmut Sandrock, the general secretary of the German Football Association (DFB), left his post on Friday, saying he wanted to allow the governing body to make a "complete new start."
Sandrock's resignation comes only one week prior to the release of the Freshfields report looking into the 2006 World Cup scandal, and with the new DFB president to be elected in April.
The 59-year-old, who had held the role since 2012, resigned with immediate effect and said on the DFB's official website: "It's just good style and common to give a new president the opportunity to also him to nominate a new general secretary for election."
Sandrock had worked for the DFB as tournament director in the build-up to the 2006 World Cup. He later had stints with RB Salzburg and FIFA, where he coordinated the Club World Cup in 2006 and 2007 as well as the Confederations Cup in 2009 and the 2010 World Cup.
On March 4, the DFB is set to release the Freshfields report, looking into the events surrounding the controversial vote for Germany to host the 2006 World Cup, which took place in 2000.
The scandal had prompted the resignation of Wolfgang Niersbach as DFB president in November. A new president is to be elected in mid-April, with 54-year-old Reinhard Grindel the only candidate for the job.