The bomb at a fish shop on Belfast's Shankill Road on 23 October 1993 killed nine Protestants and IRA bomber Thomas Begley.
On the poster, displayed on Tuesday morning, were the words "Walk of Shame", attached to photographs of the bomb victims.
It followed a death threat made against Catholic parents by loyalist paramilitaries.
Residents from the Glenbryn area, where the school is situated, have been protesting at the school for seven weeks because of alleged attacks by the larger Catholic community in Ardoyne.
The protesters held up the banner in silence as police in riot gear escorted schoolgirls and their parents along Ardoyne Road to Holy Cross primary school.
'Sombre note'
The residents later held a memorial service for the bomb victims on the Ardoyne Road
.
Residents' spokesman Stuart McCartney said the protest had taken a more sombre note.
"There's a lot of people here who lost family or were very close to people who lost their lives," he said.
"It is important that we commemorate it and honour the people who lost their lives."
The pupils have been escorted past the loyalist protesters by the security forces every day since the beginning of the school term.
The placard and whistle protest has been relatively peaceful in recent weeks, but it erupted into violence at the beginning of September.
Threat of violence
Sinn Fein's Gerry Kelly said the Catholic parents had taken a death threat made against them by a loyalist grouping very seriously.
The Red Hand Defenders, a cover name used by the Ulster Defence Association and the Loyalist Volunteer Force, said it would take "military action" against parents who walked up the road on Tuesday morning.
Mr Kelly, a north Belfast assembly member, said the parents discussed the threat before the school run.
"Generally they came to the conclusion that, whatever about the death threats, it is there to stop people going up this road so they walked up the road as they've done for a number of weeks now.
"They decided that they were not going to be intimidated out of this," he said.
The Northern Ireland Office, local politicians and church leaders have been involved in trying to resolve the dispute.
But despite recent meetings talks, no resolution has yet been reached.