The announcement reflected heightened security fears following the attack, which officials said looked like the work of al-Qaeda, and came amid raised diplomatic tension between Pakistan and the United States.
More than 60 children will be withdrawn over the next few weeks, the Foreign Office said.
They are all aged under eight, as older children tend to attend boarding school in the UK.
"Following a review of security in the wake of the attack on the Marriott Hotel, the Foreign and Commonwealth office has decided that the children of UK-based staff at the British High Commission in Islamabad should return to the UK," a spokesman said.
Any dependents, such as spouses, could return to Britain if they chose.
The spokesman said the "core work of the High Commission will not be affected. The UK is committed to maintaining its strong relationship with Pakistan, especially at this difficult time".
"The attack on the Marriott Hotel reinforces our shared determination to tackle violent extremism," he said.
At present, Britain advises its citizens to avoid all non-essential travel to Islamabad, Rawalpindi, Karachi, Lahore and Peshawar, and cautions against using international hotels popular with Westerners.
Agencies
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