The Foreign Office said there was a "specific threat" identified to Westerners in the territory, known as Somaliland, and they should depart immediately.
UK nationals have been advised for some time to avoid the breakaway territory because of the high threat of criminal and terrorist kidnappings.
A number of individuals with dual nationality are thought to travel there regularly, however, and some aid agencies are also believed to have staff there.
"We are now aware of a specific threat to Westerners in Somaliland, and urge any British nationals who remain there against our advice to leave immediately," the Foreign Office said. "As our travel advice continues to make clear, kidnapping for financial or political gain, motivated by criminality or terrorism, remains a threat throughout Somalia."
Last week, a similar threat was issued for Britons living in the Libyan city of Benghazi after the Foreign Office became aware of a "specific and imminent threat".
Tensions have been especially heightened since the Algerian hostage crisis and French intervention in Mali.
French military action in Mali, which has received British logistical support, has raised the threat of retaliatory strikes on Westerners.