The 19-year-old midfielder has signed a three-year contract with Bremen and joins the club for an undisclosed fee.
“I simply had to do something new for my development,” said Kroos.
“My aim is to become a Bundesliga player and to train with so many stars at Werder will take me forward and I am proud to be able to play for such a club.”
“We will work together on ensuring Felix can develop successfully with us,” said Bremen first-team coach Thomas Schaaf.
“In the mid-term, we have quite a bit of hope in him.”