Werner was an integral part of one of the nation's best defenses this season, registering 40 tackles and 13 sacks.
"I'm grateful to Coach (Jimbo) Fisher and Florida State for giving me the opportunity to be a Seminole and play for one of the top college football programs in the country," Werner said in a statement released by the school. "I've learned so much from the coaches, especially Coach (D.J.) Eliot, and have been able to play with some of the best players in the country.
"After sitting down with my wife, Denise, and gathering as much information, I've decided to move on and enter the NFL draft. I've enjoyed my time at FSU and will cherish the time I spent as a Seminole."
The 6-foot-4, 255-pound Werner is rated as the eighth-best player by ESPN's Scouts Inc. He is expected to be a top-10 pick in April's draft.
Werner was a German exchange student who played only two years of football in the United States before being discovered at a prep school in Connecticut. Werner burst onto the scene as a sophomore at Florida State with 37 tackles, including seven sacks. Werner is a power rusher with quick feet and a relentless motor.
"I'd like to congratulate Bjoern on his decision to enter the NFL draft," Fisher said. "It's the best decision for him and his family. Not only is he a great football player, but he's an unbelievable person. His leadership on and off the field will impact this program for years to come. I wish him nothing but the best, and he will always be remembered as one of the great players in FSU history."
Junior safety Lamarcus Joyner announced Thursday that he will return to Florida State for next season.
Information from ESPN's Joe Schad and NoleNation's David Hale was used in this report.