The 42-year-old has stepped up from coaching the under-17s to replace Huub Stevens, who was sacked on Sunday.
Keller, who has been put in charge initially until the end of the season, told the club's website: "When I was unveiled as under-17 coach in summer I never thought I'd take charge of the first team here.
"I was simply looking forward to an exciting challenge in the youth set-up. Working with the under-17s over the last few months has been great fun. The boys are eager to learn and have had a fantastic season so far.
"The biggest difference between youth football and professional football is that the game is even faster at this level. The intensity is almost the same, however. We trained under virtual professional conditions with the under-17s."
Keller's only previous Bundesliga coaching experience came in an ill-fated two-month spell in charge of Stuttgart early in the 2010/11 season.
On that occasion he stepped up from assistant coach and was thrown right into a hectic run of fixtures.
Keller reckons this time will be different because he will have time over the winter break to help put his stamp on the squad.
"Back then I was promoted from assistant coach to head coach and had eight games in the first four weeks," he said.
"Because of the busy fixture list it was virtually impossible to give the team new impetus. It's different this time because I'll have more time with the players after the cup game and I wasn't part of the senior coaching staff like I was in Stuttgart."
His first game in charge of Schalke will be a DFB-Pokal clash at home to Mainz and he said the players have responded well in training.
"The players gave me a positive reception and I could tell they were totally focused on the cup game." he said.
"Though I've watched the first team train on a regular basis, looking on from a distance is not the same as being in charge yourself. I'm now going to spend time considering how best to approach the game against Mainz.
"If we are to do well the psychological side of things will be very important."
Schalke general manager Horst Heldt said the club decided not to make an external appointment because they had a ready-made replacement in Keller, whose under-17 side have a 100% record this season.
Heldt said: "He was immediately prepared to take the job on.
"I know Jens from my time at Stuttgart (where Heldt was general manager) and am convinced he's an outstanding coach. He was a pro himself and has a wealth of experience. We hope he can deliver the impetus to get us back on track. We have every confidence in him.
"Why should we look further afield when we have good people here?"
On whether Keller will continue to lead the first team beyond the end of the season, Heldt added: "We'll wait and see how things develop and intend to manage the footballing side of things together for the time being.
"Our objective for the season remains automatic qualification for the group stage of next year's Champions League."