Members of the group set up a stall at the event in Grangemouth High School on Tuesday, which was attended by charities and voluntary groups. However, they were later asked to leave.
A spokeswoman for Falkirk Council said no political groups had been invited to the event, but said staff had “inadvertently” given permission for Yes Scotland to attend.
A spokesman for Yes Scotland said: “Yes Grangemouth were given permission by Falkirk Council to set up a stall at the school youth fair.
“It would appear they were asked to leave halfway through the event because the No campaign was either unable or disinclined to take part and there was a complaint made alleging imbalance.”
Sixteen and 17–year–olds will be able to vote for the first time in next year’s referendum, and teachers have been warned to remain impartial when discussing the vote in lessons.
Earlier this year, the head of the Educational Institute of Scotland accused campaigners on both sides of attempting to “exploit” school pupils.