The defensive midfielder, who has yet to play for Leverkusen since joining them in 2011 and is on loan at Borussia Moenchengladbach this season, won the World Cup with his country in Brazil in July.
"With the return of Christoph Kramer (next summer) we have succeeded in our concept of developing young and talented players at other clubs," said Leverkusen CEO Michael Schade.
Kramer, seen as a natural replacement to Leverkusen captain Simon Rolfes who is retiring at the end of the season, said a few months ago that the way players were treated by clubs sometimes reminded him of the "slave trade".
That triggered an angry reaction from Leverkusen officials but the 23-year-old, who has also had a loan spell at VfL Bochum, said he was now ready to play for his parent club.
"I have known Bayer since my youth and always dreamt of making it among the pros," added Kramer. "I have now succeeded in that via Bochum and Gladbach and I am very happy."
Leverkusen meet Atletico Madrid in the last 16 of the Champions League in February.
(Reporting by Karolos Grohmann, editing by Tony Jimenez)
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