"Religiously aggravated harassment is an unusual offence, the first I have dealt with, especially one where perhaps not everyone would consider it a religion, but it is deemed to be so.
"He did not know it constituted religious aggravation and pleaded guilty at the earliest opportunity."
Colchester Youth court heard how the teenager, from Lawford, north east Essex, harassed the McDonald's employee between December 24 last year and February 18.
He repeatedly went into the restaurant in High Street, Colchester, to "tease" his victim, leading to the staff member becoming "very upset about it".
Under section 32 of the Crime and Disorder Act 1998, a person is guilty of an offence if found to have committed "racially or religiously aggravated" harassment.
Paganism encompasses a wide variety of religious groups, including druids and shamans who worship different deities, and is recognised in law. Some concentrate on witchcraft or ecology.
The Pagan Federation of Great Britain says that those who practice the belief are free to "pursue their own vision of the Divine as a direct and personal experience". It defines Paganiosm as a "nature-worshiping religion" which incorporates a "rich diversity of traditions".
Sitting at the youth court on Wednesday, magistrates handed the teenager a three month referral order for religiously aggravated harassment.
He was ordered to report to a panel of youth workers and told he may be required to do unpaid work. The bench also imposed a restraining order banning contact between the boy and his victim until November this year.
Laura Austin, mitigating, told the court: "He is apologetic and did not realise paganism was a recognised religion.
"The teasing was going to a level where the victim got very upset about it. His parents are not happy with him and have imposed their own curfew. You do wonder if the employers could or should have done more to prevent the behaviour."
Following the hearing Miss Austin added: "As far as I'm aware this is the first case of its kind and I had to make a number of enquiries to satisfy myself that it was a recognised religion as far as the legislation is concerned."
Cas Morehan, the franchise holder of the McDonald's store, said: "Unfortunately there are instances where staff are subjected to harassment and abuse by customers.
"As a diligent employer we recognise our duty of care to our employees and will take whatever action we deem necessary to protect our staff. In this particular instance we needed to involve the police in what has occurred."