The Germany international is currently on a two-year loan at fellow Bundesliga club Borussia Monchengladbach - a deal that is set to expire at the end of the season.
World-Cup winner Kramer has been linked with a permanent switch to Borussia-Park after impressing during his time with Gladbach.
However, the 23-year-old midfielder will return to Leverkusen ahead of the 2015-16 campaign and has penned fresh terms on a contract that runs until June 2019.
"After talking with those responsible in Leverkusen I did not hesitate to extend my contract," Kramer told Leverkusen's official website.
"The total package with the team, the coach and the club itself just fits. I have known Bayer since my youth, it was always my dream to make it in the [first-team] squad.
"That I have managed that via a detour at Bochum and Borussia Monchengladbach is a great feeling of happiness for me."
After committing to Leverkusen, Kramer took time to thank Gladbach for helping him develop into a full international.
"I have become an international at Monchengladbach," he added. "For this and for the wonderful time I am very grateful.
"I will do everything in the remaining six months to help the club play internationally again."
Leverkusen's decision to keep Kramer will help to negate the loss of captain Simon Rolfes, who earlier this month announced his decision to retire at the end of the season.
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