Parents at the school in Coventry reportedly raised concerns after the asylum-seeker student, who appeared to be a balding, adult male - joined the school in October.
The asylum-seeker is said to have moved to the UK from Gambia, West Africa.
The Home Office launched an 'urgent investigation' into the matter after the city council wrote to parents to reassure them about the situation.
The pupil is said to have not returned to classes after October half-term, according to The Sun newspaper.
One parent said: 'The general feeling among parents is that they are bemused and untrusting. Parents have been told that sharing images of children is wrong and is a form of bullying, they've not been told what action was taken.'
Photos of the student were posted on Facebook after one schoolgirl shared the images in a private Snapchat questioning his age.
The girl's mother said she was then called into school to discuss the issue with teachers and that they were concerned sharing photos of the new classmate amounted to bullying.
She told The Sun: 'I said, 'You can't really blame the children [for talking about it] - he looks about 40'. They sort of nodded and said, 'Yes – we did have concerns but we've been told that he is in fact Year 11 age'.
'I just felt a bit annoyed that the school was trying to shut down my daughter. I said, 'I'm all for encouraging free speech and I don't agree that it was bullying as such.'
She added: 'The school has said it's inappropriate for us to question his age. There's absolutely no way this boy looks 15. He looks about 40 to me.'
Another parent told Metro: 'Pupils were coming home saying there's a man in our class, some were even saying they reckoned he could be aged up to 40.
'He has a thin hairline and apparently he has no birth certificate or passport. He might be the right age, he might not. Either way parents would like some clarity.'
Coventry City Council was forced to send a letter to parents after the pupil took his place in classes.
Sarah Mills, head of education entitlement at Coventry City Council, said in the open letter: "When pupils arrive in England and present an application for a school place, we - local authorities and schools - are obliged to process these applications.
"If there are concerns or doubts regarding a pupil’s age at the time of application, schools and local authorities are able to ask for further evidence in the form of birth certificates and passports.
"However, please note, on some rare occasions if pupils arrive as asylum seekers and alone, i.e. without parents, these may not always be available.
"I am able to confirm [the school] follows all of these procedures and always seeks the city council's support in such matters.
A school spokesperson later told The Sun they had been able to verify the student's age - but couldn't reveal how.
