The 51-year-old worked alongside Germany coach Joachim Loew with the national team from 2006 to 2014, culminating in the World victory in Brazil three years ago.
"I have spent a successful but also intense 10 years at the DFB," Flick said in a statement. "There are at the moment neither other sporting ambitions now were there any problems.
"The only reason is my personal wish to focus more on my family in the future," said Flick, whose contract ran to 2019.
During Flick's time with Germany they reached at least the semi-finals in every major tournament. He switched to the role of DFB sports director in 2014.
"In his 10 years at the DFB, Hansi Flick earned a lot of honours for German football," DFB President Reinhard Grindel said.
"Working with Joachim Loew he played a key role in the World Cup win and then as sports director laid the foundations for the future."
Flick will be replaced on an interim basis by former Germany youth coach Horst Hrubesch with a permanent successor due to be announced in September.
(Reporting by Karolos Grohmann, editing by Ed Osmond)
