About 40 Lancaster Royal Grammar School students, from Garstang and surrounding villages, were told they could no longer get on their usual bus because it was now exclusively for the use of Lancaster Girls' Grammar School pupils.
And they were even more confused when the alternative buses were either full or stopped in Lancaster town centre – leaving them with a 10 minute walk up to school.
James Flesher, 15, who has been getting a bus from Bonds Lane for four years, said his friends had been threatened with the police after getting on the wrong bus.
He said: "The driver announced that the bus was no longer allowing boys on it, not due to behaviour or anything of that sort, but because it was supposedly too full.
"This was completely untrue, and many people were able to have two seats to themselves.
"We were told about the changes a week after school restarted, as opposed to when we ordered bus passes for the service. We weren't notified until the incident happened – no letters were sent to parents or to the school explaining the situation."
Tony Cresswell, inspector for Stagecoach, said teachers and inspectors had together assessed a problem with overloading and had come to the decision to split the buses by gender.
Mr Cresswell said the school had been informed of the changes.
But Ian Whitehouse, deputy head at Lancaster Royal Grammar, confirmed the school had received complaints from parents over buses.
He said he was not aware of any communication from Stagecoach but added he hoped to discuss the issue with parents and Stagecoach soon.