Special prosecutor Angela Corey announced the charges but would not discuss how she arrived at them or disclose other details of her investigation, saying: "That's why we try cases in court."
Second-degree murder is typically brought in cases when there is a fight or other confrontation that results in death and but does involve a premeditated plan to kill.
Corey would not disclose Zimmerman's whereabouts for his safety but said that he will be in court within 24 hours.
Zimmerman's new attorney, Mark O'Mara, said: "I'm expecting a lot of work and hopefully justice in the end."
Zimmerman, whose father is white and whose mother is Hispanic, has asserted since the Feb. 26 killing in Sanford that he shot in self-defense after the teenager attacked him. Martin's family argued Zimmerman was the aggressor.
The shooting brought demands from black leaders for his arrest and set off a furious nationwide debate over race and self-defense that reached all the way to the White House.
Corey said the decision to bring charges was based on the facts and the law, declaring: "We do not prosecute by public pressure or by petition."
Second-degree murder charge in Trayvon Martin case
Let Justice Prevail.