Police are investigating claims the thief struck twice at Leith Academy, making off with 18 mobile phones.
Last Friday, items were stolen from the girls’ changing rooms while a group of S3 pupils were taking part in PE lessons.
On Monday, it is claimed the culprit hid in a shower area while a group of boys were getting changed.
A concerned former pupil with a sibling at the school, who asked not to be named, said the incidents showed security at the school needs to be improved.
“Those girls were only 13 of 14 years old – this could have been a much more serious incident.
“The fact it has happened twice in a week shows you the security there needs to be tightened up. The first time it was in the girls’ changing room.
“Pupils had noticed their phones and things had gone missing – they reported it to the PE teacher and it was passed on to the management.
“When the CCTV was checked they saw him. Apparently he had covered himself up. He was wearing a long jacket and a scarf.
“He must have known the layout of the school because he knew exactly where the changing rooms were and he knew when the kids were going to be doing PE.
“A lot of the pupils are paranoid now – they know he has been in the changing room while they have been getting changed.”
The community school –which has almost 1000 pupils – hosts adult education classes, some of which take place during school hours.
The former pupil added: “You can just walk in through the front door, they never make anybody sign in or out.
“The school has not contacted the parents about this or anything – I think it is trying to keep it under wraps.”
A spokeswoman for Edinburgh City Council said: “I can confirm that a man entered the school and we now believe he stole mobile phones from the PE changing rooms.
“The matter is currently being dealt with by the police.”
Lothian and Borders Police said: “Police are following a positive line of inquiry following the theft of property from a school in Edinburgh.
“Around 18 mobile phones have been reported stolen from Leith Academy between Friday, March 9 and Monday, March 12.
“Officers are conducting inquiries to identify who is responsible as well as working with staff and pupils to provide crime prevention advice to prevent any other incidents.”