The five-second video was posted online this week. It shows the uniformed officer slapping a young man three times -- one slap loud enough to hear a pop -- and then kicking him while yelling profanities.
The incident happened Tuesday on the grounds of Reach! Partnership School in Baltimore, school officials said.
The officer seen striking the youth and a female officer standing behind him have been placed on paid administrative leave, said Karen Parks, spokeswoman for the Baltimore public school system.
The officer is under investigation for assault and misconduct, officials said.
"As a parent of a Baltimore city school student, I was appalled by what I saw," Mayor Stephanie Rawlings-Blake said of the video. "The behavior that was demonstrated ... is certainly something you never want to see. ... Certainly not a school officer acting in this way, particularly with a young person."
Baltimore School Police Chief Marshall Goodwin was also placed on paid administrative leave pending an investigation, said Parks, describing the move as a "personnel matter."
Parks said the unidentified young man who was slapped was not a student at the school, and officials were trying to figure out whether he was enrolled in Baltimore's school system.
"His presence at the school and the series of events before and after the incident are currently under investigation," the city school system said, referring to the young man.
Lauren Geisser, an attorney for the teen and his parents, said she has documentation identifying him as a 10th grader at the school. She said he suffered face and rib injuries. The young man has not been interviewed by police, she said.
"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 the statement. "Our school police officers are entrusted with ensuring the safety of our students and staff, and I know that most of them take this job seriously while maintaining a high level of professionalism. The behavior in the video is completely unacceptable."
Akil Hamm, acting chief of the Baltimore school police, said the "excessive force" displayed in the video was "very troubling."
Michael Davey, attorney for the officer who struck the young man, said his client was responding to a call of an intruder on school grounds.
Davey said the online video captures only a few seconds of an encounter that played out over several minutes.
The young man became belligerent and angry after the officer repeatedly asked him to leave, according to Davey, who said the earlier part of the encounter does not appear to have been captured on video.
Geisser said she had no information about her client's response.
"One would expect that police officers that are specifically charged with protecting children would exercise restraint, care and understanding when dealing with these children," she said. "Instead, these officers used their powers to inflict harm on a student who was trying to attend school lawfully."
The officer's behavior in the video has been widely criticized.
Karl Perry, the chief school supports officer, said, "I'm a parent, and I'm totally appalled at what I saw in that video."
Another man, Gary Payne, who was interviewed near the school, told CNN affiliate WJZ
: "If it was my son, I would be highly upset, asking questions, wanting to know what happened prior to it. But still, nobody deserves to get ... hands put on them like that."
Baltimore school police officers not only patrol the schools but also investigate offenses, counsel students and advise school staff on security issues, according to the district's website.
According to Maryland law, school police officers have all the powers of state peace officers and receive the same academy training as city police officers, the website said.
A coalition of Baltimore activists held a news conference Wednesday to condemn the actions of the school police officer.
Thena Robinson Mock, project director of the Advancement Project's Ending the Schoolhouse to Jailhouse Track, said the video was part of a "horrific pattern of ... brutality against youth of color" in the nation's schools.
"We have a problem with police in schools," she said. "We need to truly examine our approach to the role of police officers in schools. ... This is not a discipline or policing crisis. This is racial justice crisis."
Both officers in the video and the young man appear to be black.
Some 43% of all U.S. public schools -- including 63% of middle and 64% of high schools -- had school resource officers on their grounds during the 2013-2014 school year, the National Center for Education Statistics noted in May.