Aaron Bond, 14, used his skills to access confidential information about staff and students, even looking up the vice-principal's financial information.
Using passwords, he managed to look at details about his peers and was able to edit the IT room booking system and school newsletter before the security breach was spotted.
He has now been visited by police, who took DNA samples and fingerprints before giving him a formal reprimand.
His school, King Edward VI College in Totnes, Devon has permanently expelled him and maintains no student should have had access to passwords.
Aaron, who is predicted A*, A and B grades in his GCSEs, said: "I am very sorry and if I had known the consequences I never would have done it."
The teenager, who has designed six apps used on smartphones and is the managing director of his own web design company,was among hand-picked delegates at the Apple conference last year.
He is already being considered for university courses because he is so advanced with computers, and said he was "curious" about whether he could hack the school's system.
He claims he infiltrated the computers after seeing a list of passwords displayed on a white board in the school's IT room, but the school insists no-one within the school would have had access to them.
Even after the breach was spotted and the system locked down, he was still able to get in to the vice-principal's financial records.
He said: "I was a bit scared and curious and I wondered if I would be able to get in again."
Aaron was originally suspended for five days as police were called in, and Aaron gave DNA samples, fingerprints and had a photo taken at Totnes police station.
His mother Kate, 36, said Aaron was curious, "like any school boy would have been."
She said: "I think the security of the school computer system should be a lot better.
"A 14-year-old boy should not have been able to get into the system.
"I don't see why they can't give Aaron a second chance."
He has now lost an against his exclusion and has started at a new school.
Principal Kate Mason confirmed Aaron admitted accessing the school's IT system without permission on several occasions.
She said: "The password information Aaron said he saw were examples but provided an initial idea which Aaron then used to interfere with school systems and access other accounts.
"No one has access to staff passwords.
"Aaron was excluded from the college in accordance with the serious nature of the offence and the college's behaviour policy and acceptable user policy, which he had signed."
A spokesman for Devon and Cornwall police said the formal reprimand was a warning
"Although it's not citable - the reprimand is a warning about his behaviour," he added. "It's like a slap on the wrists."