Mertesacker will take up the role from January 1, 2027, succeeding Andreas Rettig, who is stepping down at the end of the year for personal reasons.
The 2014 World Cup winner has signed a contract running through to after the 2030 World Cup, matching the length of Klopp's own deal as head coach, and will oversee the DFB's national team and academy structures as one of four senior figures in the federation's restructured leadership team.
Three successive disappointing World Cups have prompted the DFB to rethink its organisation beyond the coaching position alone, with new figures also being brought into other senior roles as part of a wider shake-up of the federation's leadership structure.
The federation officially confirmed the deal on Friday, with the contract signing due to take place the same day, though Mertesacker will not be present at Friday's press conference introducing Klopp as Germany's new head coach at the DFB's Frankfurt headquarters.
The former Arsenal and Werder Bremen defender made 104 appearances for Germany during a playing career that also included a World Cup semi-final in 2006 and 2010 and reaching the final of Euro 2008. After hanging up his boots, Mertesacker spent eight years running Arsenal's academy, overseeing the development of a generation of young talent at the London club before stepping away from the role earlier this year to explore new challenges, most recently working as a pundit for German broadcaster ZDF during this summer's World Cup.
The DFB's decision to bring in a decorated former international to oversee sporting matters reflects a broader push to rebuild confidence in the national set-up after a turbulent period, with Klopp's arrival as head coach seen by the federation as the first major step in a longer process of renewal.