Officer Edward Nero is one of six officers facing charges in the Freddie Gray case and was found not guilty of second-degree assault, reckless endangerment and misconduct in office.
Baltimore Mayor Stephanie Rawlings-Blake called for calm following the verdict and said Nero would face an administrative review by the police department.
"This is our American system of justice and police officers must be afforded the same justice system as every other citizen in this city, state and country," she said in a statement, Al Jazeera reported.
The trial of another of the officers ended in a mistrial last year when the jury could not reach a conclusion, and Nero had opted instead to have a judge hear his case.
Gray suffered a severe neck injury after his arrest on April 12 last year, apparently while being transported in the back of a police van.
He complained about breathing difficulties, fell into a coma and died one week later. The 25-year-old had been taken into custody for carrying an illegal switchblade.
Gray's death was one of several recent killings of African American men by police officers that touched off demonstrations in the United States.
Nero's acquittal raises questions whether prosecutors will proceed with the trial of four other officers, whose charges are still pending.
The police union supporting Nero has reportedly urged the government to drop all the charges.