Councillors have voted to recommend the closure of Bath's Culverhay School.
Bath and North East Somerset (Banes) council's cabinet recommended that two other secondary schools, Broadlands and St Mark's, should remain open.
Oldfield Girls School, which was also threatened with closure, has said it will apply to become an academy.
Pupils and teachers demonstrated outside the city's Guildhall while the vote on plans to close two schools and open two new ones took place inside.
The all-boys Culverhay School is around half full and had wanted to introduce girls.
A consultation on the recommendation to close it will now be held.
The council has said the changes are aimed at improving standards and educational outcomes over the next 20 years.