Anthony C. Spence, the officer seen hitting the youth in the video,
faces charges of child abuse, assault and misconduct in office, court documents state.
Fellow Officer Saverna Bias has been charged with assault and misconduct in office. The video was recorded at the city's REACH Partnership School on March 1, school officials said.
According to the Baltimore Police Department, both officers turned themselves in on Tuesday night, posted bond and were released. They are due back in court on April 7, according to the court documents.
Attempts by CNN to reach both officers for comment were not immediately successful.
Baltimore schools top police officer placed on leave
Marshall Goodwin, chief of police for Baltimore City Public Schools, has been placed on paid administrative leave, said Karen Parks, a spokeswoman for the Baltimore public school system.
The day after the incident, Lauren Geisser, an attorney for the teen and his parents, said she had documentation identifying the youth as a 10th-grader at the school. She said he suffered face and rib injuries.
"The boy had a right to be at the school where he was an enrolled student," she said.
"With respect to refusing to leave the school, the student didn't want to leave the school where he had a right to attend."
Baltimore police and State's Attorney's Office are handling the criminal investigation, officials said.
"I am completely appalled and disappointed by what is depicted in the video," the school system's CEO, Gregory Thornton, said in a statement.
Akil Hamm, acting chief of the Baltimore school police, said the "excessive force" displayed in the video was "very troubling."