He killed eight fellow students and a school guard before calling the police and being arrested.
The shooter first killed a school guard and then three students in a hallway, according to senior police official Veselin Milic.
He then entered a history classroom that was close to the school entrance and opened fire again, Milic said.
The assailant called police himself when the attack at the school in central Belgrade was over although authorities had received a call reporting the shooting two minutes earlier.
A father of a student said the shooter entered his daughter's classroom, firing at her teacher and then her classmates as they ducked under their desks.
Most students at the school were able to flee through a back door, according to a local official.
While Milic said the shooter planned the attack for a month, sketching classrooms and writing out a list of children he planned to "liquidate," authorities said they did not know the motive for shooting.
It was unclear if he shot any of the people that he named on his list.
The rarity of such attacks in Serbia added to the shock many felt.
Commentators on television and officials repeatedly said it was the kind of thing they expected to read about elsewhere, particularly in the United States.
Authorities declared three days of mourning, starting on Friday.
Police identified the shooter as Kosta Kecmanovic, who attended the Vladislav Ribnikar school, where students would typically range in age from six to 15.
The Belgrade prosecutor's office said Kecmanovic cannot face criminal charges because he is under the age of 14.
Social services will determine what happens to him.
He carried two guns belonging to his father - at least one a handgun - and four Molotov cocktails, officials said.
Interior Minister Bratislav Gasic said the weapons were licensed and kept in a safe but that the teen, who had been to shooting ranges, apparently knew the code.
The father was also arrested but has yet to be charged.
It is not clear how many rounds were fired but police said the shooter reloaded the handgun.
In addition to the nine killed, six children and a teacher were also hospitalised.
Local media footage showed a commotion as police removed Kecmanovic, whose head was covered as officers led him to a car.
Police sealed off the blocks around the school.
Authorities later carried body bags to a waiting van.
Police said they received a call about the shooting about 8.40am on the first day that classes resumed after a long weekend for the May 1 holiday.
"I was able to hear the shooting. It was nonstop," said a student who was in a sports class when gunfire erupted elsewhere in the building.
Her mother asked that her name be withheld because of her age.
"I didn't know what was happening. We were receiving some messages on the phone."
The student described the shooter as a "quiet guy" who had good marks.
"He was not so open with everybody. Surely I wasn't expecting this to happen," she said.
Milan Nedeljkovic, the mayor of the Belgrade area of Vracar where the shooting happened, said most of the students were removed from the school through a back door.
"We have video surveillance but now this is a lesson - we need metal detectors too," he said.
"It is a huge tragedy... something like this (happening) in Belgrade. Such a tragedy at a primary school".
