Wearing handcuffs and a dark grey jumpsuit, Zimmerman appeared in a Seminole County courtroom for the brief hearing before Judge Mark E. Herr, who was not in the courtroom but spoke through a closed-circuit TV connection.
Herr said he found probable cause to proceed with the case against Zimmerman and set the date for arraignment for May 29 at 1:30 p.m. before another judge.
Throughout the four-minute hearing, Zimmerman stood up, looked straight ahead and said only "Yes, sir," twice when asked questions about the charge against him and about his attorney Mark O'Mara.
His hair was shaved and he had a thin goatee.
"He's tired, it's been a very long period of time for him, and he's gone through some tribulations of his own being the focus of the intensity of this event," O'Mara said after the appearance. "He is facing second-degree murder charges now, he's frightened. That would frighten any one of us."
O'Mara has said his client will plead not guilty. He also asked Herr to seal documents in the case.
"My concern, before I was involed in the case, was that this matter was being handled in a piecemeal fashion, whether it was police, law enforcement, defense, other witnesses, people who just wanted to be involved in the case, people who saw things," O'Mara said, when asked why he wanted the case sealed.
O'Mara said after the hearing that he'd file a bond motion at a later time. Zimmerman spent the night in jail and is in protective custody, O'Mara said.
"He's glad the process is in place, he really does hope, as the prosecutor said, that we're given the opportunity by the media, by the community, to handle this case the way it's supposed to be handled," O'Mara said.
The prosecutor handling the case, Bernardo de la Rionda, said after the hearing that the second-degree murder charge was appropriate.
"It's our obligation under the law to only file charges we can prove, second-degree murder we felt was an appropriate charge and that's why it was filed," de la Rionda said. "I'm not going to get into the facts."
O'Mara said he's not currently taking attorney's fees from Zimmerman.
"Obviously it was a horrible intersection of two young men's lives and it ended in tragedy," O'Mara said. "We have to figure out how it happened, why it happened and who might be responsible for it."
Later Thursday, the Seminole County Sheriff's Office said Zimmerman was being segregated from the general population because of the high-profile nature of the case. A list of his commissary purchases was also released and it included soap, playing cards, and crossword puzzle book.
Click here for the list of items.
The 28-year-old turned himself in and was booked into the Seminole County jail Wednesday night, after State Attorney Angela Corey announced the charges at a news conference in Jacksonville.
Wednesday's dramatic turn of events came 45 days after Zimmerman shot Martin in a gated community in Sanford in what Zimmerman said was self-defense.
Martin was visiting with his father at his father's girlfriend's home in the gated community and was walking back from a 7-Eleven when he was shot by Zimmerman, a neighborhood watch volunteer, on the night of Feb. 26.
Zimmerman had spotted the teen and called 911, telling the dispatcher he was following Martin. The dispatcher told him not to, but Martin and Zimmerman got into a confrontation.
Zimmerman said he shot Martin, who was unarmed, in the scuffle, police said.
Police said Zimmerman had a bloody nose, gash on the back of his head and grass stains on the back of his shirt. His family also claims his nose was broken in the attack.
The Martin family and their attorney say Martin wasn't the aggressor and claim race played a factor in the shooting. Martin was black, while Zimmerman is a biracial Latino.
The Sanford Police Department came under withering criticism for not arresting Zimmerman in the weeks after the shooting. Martin's parents, their attorney and activists pushed for an arrest as outrage grew around the country. Numerous rallies were held in Sanford and cities around America, and "I am Trayvon Martin" became a rallying cry.
Sanford Police Chief Bill Lee Jr. was forced to temporarily step down, acknowledging that his presence as the chief had become a distraction, while standing by his department and its investigation. He had said there was no probable cause to arrest Zimmerman, citing the state's controversial "Stand Your Ground" law.
Corey, based in the Jacksonville area, was appointed the special prosecutor in the case by Gov. Rick Scott on March 22 after State Attorney Norm Wolfinger, whose district covers Sanford, recused himself.
At Wednesday's news conference, Corey said she and her team of investigators didn't come to the decision to charge Zimmerman lightly.
"We do not prosecute by public pressure or by petition. We prosecute based on the facts of any given case, as well as on the laws of the state of Florida," Corey said.
"I hope that Ms. Corey did what she's supposed to do, I think she did, which is look at the case as a prosecutor, charge the highest crime that she thinks she can and did it appropriately, I have no reason to believe otherwise," O'Mara said during an appearance on NBC's "Today Show" Thursday.
Zimmerman's brother expressed his displeasure with the prosecutor's decision on CNN Wednesday night, saying he would have hoped for "the more courageous tactic, which would have just been simply to say we’re not prosecuting, and here’s why.”
“This is an unfortunate outcome, but we’re a strong family," Robert Zimmerman Jr. said. "We are prepared for it, and we’re prepared for the rest of our American justice system to have its say in what ultimately should work out, in the end, to exonerate my brother."
Students at Miami's Krop Senior High School, where Martin was a junior this year, supported the charge against Zimmerman.
“I was happy because I think Trayvon’s family will have some peace. And now the next step is just to find him guilty," one student said, adding that she hoped Zimmerman is convicted so his parents can be at peace and "their pain can ease."
Martin's parents said Thursday that they were relieved Corey decided to charge Zimmerman.
"Finally the person that shot and killed our son was going to be held accountable for what he has done, that's what went through my mind the moment I heard the charges," mother Sybrina Fulton said during an appearance on the "Today Show" Thursday. "We just want him to be held accountable for what he's done. By him not being arrested, that would not have been done, we are happy that he was arrested so that he can give his side of the story."
Father Tracy Martin said he was also pleased with the arrest but said it should have happened weeks ago.
"Had the Sanford Police department did a thorough and impartial investigation from the beginning, George Zimmerman would have been locked up from day one and there wouldn't have been such a huge public outcry for the arrest," he said. "If in fact we had to plead our case to public officials just to get him arrested, if that's what we have to continue to do to plead our case, that's what we'll do, but he should have in fact been arrested from day one."
Fulton said she'd like an apology from Zimmerman.
"One of the things that I still believe in, a person should apologize when they are actually remorseful for what they've done," she said. "I believe it was an accident, I believe that it just got out of control and he couldn't turn the clock back."
Fulton later clarified that the confrontation between Zimmerman and her son was an accident, not the shooting itself.
"When I referenced the word 'accident' today with regard to Trayvon's death, in NO way did I mean the shooting was an accident. We believe that George Zimmerman stalked my son and murdered him in cold blood," Fulton said in a statement. "The 'accident' I was referring to was the fact that George Zimmerman and my son ever crossed paths. It was an accidental encounter. If George Zimmerman hadn't gotten out of his vehicle, this entire incident would have been avoided. My son was profiled, followed and murdered by George Zimmerman, and there was nothing accidental about that."
Fulton said that her family is still hurting from the shooting.
"I would ask him, did he know that that was a minor, that that was a teenager and that he did not have a weapon. I would ask him that I understand that his family is hurting but think about our family, that lost our teenage son," Fulton said on the "Today Show." "It's just very difficult to live with day in and day out. I'm sure his parents can pick up the phone and call him, but we can't pick up the phone and call Trayvon anymore."
O'Mara said that he looks forward to talking with her to see what her feelings are.
"We are not going to be talking about using her words against the mother of a deceased child," he said when asked about the comments.
The FBI is still investigating the shooting.
NBC 6's Ari Odzer contributed reporting.