It follows complaints from parents, pupils and staff about shared toilets at the new £47 million Lochside Academy, which opened last year in Aberdeen.
Parents have expressed their fears online about the privacy of children.
And one mum said her son was being put off attending because of the arrangement.
A questionnaire will be now be given to pupils, encouraging them to make their voices known on the issue.
The school say its unisex toilet policy may be reversed if it is shown to be unpopular.
Unisex toilets have become increasingly common in schools across the UK.
One of the first schools to adopt unisex toilets was a secondary school in Stockport in 2000 and hundreds have since followed suit.
The head teacher at the time argued that the move stopped bullying, vandalism and smoking in the toilets.
But rows have since been sparked with parents, pupils and even staff objecting.
Earlier this month, the parent council backed plans to install unisex toilets at a primary school in Fraserburgh.
Work on the £65,000 project at South Park school is due to start in the summer and Aberdeenshire Council has issued a tender for the project.
The lavatories will be completely stripped out and replaced with four brand new cubicles.
But in 2012, the local authority was forced into a U-turn over a similar plan for the new £25m Mearns Academy following complaints from parents.
Torry and Ferryhill councillor Catriona Mackenzie urged parents and guardians at Lochside to make any concerns known “as soon as possible”.
He said: “I have been made aware of concerns about the toilet facilities at Lochside Academy.
“I am confident that the school leadership is engaging proactively and positively with pupils on this issue, and is putting pupil safety and security first.
“I think it’s important that we have the information and facts in front of us, so problems can be sorted out in a measured and fair way.
“If pupils of Lochside or their parents have any concerns, I would urge them to make that known as soon as possible.”