For the past two years, the high school has raised the rainbow flag during Pride Week, which is put on by the school's Gay Straight Alliance.
"However, this year, only a few days before the planned raising of the flag, we received an email from the premier, David Alward, stating that we are not allowed to raise the pride flag due to a law that says no non-official flags can be flown on public property," states Leo Hayes student Tianna Whelan in her online petition at change.org.
The petition asks the New Brunswick government "to allow schools to raise the pride flag because the safety and acceptable of children should be placed at a higher importance than a law that was forgotten about for two years."
"Flying the pride flag shows students, and the public, that the school is a safe and accepting place for everyone."
The petition had been signed by about 100 people by Friday morning.
The gay pride flag was raised at the New Brunswick legislature to support gay athletes during the Sochi Olympics. However, it took until the sixth day of the Olympics for the flag to be raised.
"Government does not move at the fastest pace, that's for sure," said cabinet minister Craig Leonard at the time.
"But I think what's important is that the flag is flying today in solidarity with the LGBT community, and certainly we as a government want to make sure that message is sent loud and clear that we appreciate the LGBT community in this province.
Friday marks the end of Pride Week at Leo Hayes.
The pride flag is flying at City Hall in Fredericton.