Children, their teachers, and their parents who were waiting to collect them were left stunned when the pair, thought to be in their early 20s, was discovered.
A picture shows one of the men hidden in a pile of suitcases and backpacks in the hold.
Hampshire Police were called to Hounsdown School in the village of Totton where the pupils were being dropped off on Saturday.
The coach had been carrying Year 9 and 10 pupils who had just come back from a three-day trip visiting Boulogne University, about 20 miles south of Calais.
They had travelled home via the Eurotunnel at Calais, but it remains unclear how the men got on the coach.
A mum, who had been at the school to collect her daughter, told the BBC: ‘I saw one male with his hood up but I believe there were two males.’
She added: ‘My daughter came running over and she said “Oh my God, there’s people sat in where the suitcases are”.
‘Obviously it’s quite concerning because there were 36 children on the coach and no-one was aware that they were on there.
‘I understand these immigrants are wanting a better life but it is not very good targeting a coach full of children.’
Several parents took to social media to express their shock of what happened.
‘Was an absolute shocker to see a person sat there as the kids went forward to get their bags,’ one man said.
Hampshire police confirmed that officers attended but that no arrests were made.
A spokesperson said: ‘We were called just before 5.15pm on Saturday, February 10, to reports that two people, who were possibly illegal immigrants, had been found at Hounsdown School in Totton.
‘Officers have attended. No arrests have been made.’