Kerk was handed his debut on the final day of last season and has been regular from the bench in the current campaign, making 17 substitute appearances in the league.
Freiburg may have spent the majority of their time in the bottom half of the table but the 20-year-old has impressed enough to earn a new deal, although the length of it was not released.
"Sebastian is an offensive player and still has a lot of potential for development," sporting director Jochen Saier told the club's official website.
"He came to us as a 14-year-old and we look forward to partnering with him in the next step in his career."
Kerk has made six appearances for Germany's under-20 side.
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