The Discovery Academy, in Bentilee, Stoke-on-Trent, made the controversial changes this week.
Parents of pupils claim the barriers are locked during lesson times.
The issue of periods, bowel conditions and the potential impact of unpredictable upset stomachs have all been raised.
On Thursday, more than 70 pupils walked out of classes in protest of the new decision.
One mum, 30, said: ‘I was flicking through Snapchat when I saw one of the gates. I asked my son “are there gates on the toilets?” He said “yes”.
‘I phoned the office and asked them about it. I said “send my son home now”. They asked me why and I told them “because I said so, that’s why”.
‘My son asked to go to the toilet and he was told “no”. He wasn’t allowed and he has a medical pass.