The 42-year-old had been in charge of the Veltins Arena side since December 2012 and will now stay on for two additional seasons
The 42-year-old was named interim-coach in December 2012 following the departure of Huub Stevens and the Gelsenkirchen side have now opted to continue with Keller at the helm.
"Jens took charge of the team in an extremely difficult situation last December. Despite all the resistance following his appointment, he remained unperturbed and faithful to his ideas and in so doing put Schalke back on course in the Bundesliga," said general manager Horst Heldt.
"We're convinced by the work he's doing because we can see the progress made by the team in recent months despite all the injury problems.
"Jens is pursuing a coherent concept that has won the support not only of the players but also of the decision-makers inside the club."
Keller has guided Schalke to fourth place in the Bundesliga table since taking over with two games to go.