Around 250 pupils and staff were told to leave the school as police and emergency services were called to the scene at 9.44am.
The children were taken to neighbours' houses and nearby school Danderyd's Gymnasium.
The building was cordoned off while police teams investigated the site.
"First I was just wondering why someone would put a bomb in our school and I was thinking what if there actually is one or what if it is a fake?," one 11-year-old pupil, Freya Sonnorp, told The Local.
"The teachers seemed all really calm but then some of the pupils were upset, so I wasn't sure how serious it was," she explained.
An email sent to parents by the school just before 11.30am confirmed that all the pupils were out of harm's way.
"All children are safe. The school is advised by the police on site. Children are not to be collected. No one is released. We wait for further instructions," it read.
"There will be a forensic investigation of the premises to make sure they are safe," police control room officer Sven-Erik Olsson said in an interview with The Local, but added that no suspicious objects had been found.
A fire engine by the school on Tuesday. Photo: Christine Olsson/TT
Located in the suburb of Djursholm, the British International School of Stockholm provides education for up to 500 children, aged 3-13 (extending to 3-16 by 2017), of more than 45 nationalities.
"We have got emergency procedures that we use and so when children were notified that the alarm had gone off they knew what to do (...) most of them would have assumed it was a drill," the school's principal, Carl Hutson, told The Local.
"I am extremely impressed with everything – the staff and the pupils were evacuated in a really orderly way. There was brilliant help from the local community. The police acted very, very quickly, and I have been kept informed."
He declined to comment on the exact nature of the bomb threat, which police said was made by telephone to the school switchboard operator.
"I know the details but I am not going to disclose those now," said Hutson.
Children were allowed back on to the site soon after lunch to collect their bags while teaching was set to resume on Wednesday.
"I am not scared now," said Sonnorp. "I know this kind of thing very rare and is something that probably won't happen twice."
However, the British International School of Stavanger in Norway also received a bomb threat on Tuesday morning. Stockholm police would not comment on whether the two incidents were connected to each other, but their Norwegian counterparts told regional newspaper Stavanger Aftenblad that they would be looking at possible links.
"The threats occurred almost simultaneously. There was about a 10 minutes' difference between the two messages. We will investigate it further," police spokesman Einar Johannesen told the paper.
Hungarian media also reported that the British International School in Budapest had been evacuated after a bomb threat at 8.10am.