Thousands of other youngsters with disabilities are expected to benefit following the ruling in the discrimination case against South Lanarkshire Council.
Thomas Pettigrew, 10, a pupil at St Hilary's Primary School in East Kilbride, had a guitar bought for him by his parents so he could take part in the sessions, and they asked the local authority to provide him with additional support, including for assistance in using the toilet and other personal care and moving and holding his guitar.
Thomas, who has several chronic conditions that have a significant effect on his ability to carry out normal daily activities, needs help to adjust his guitar, take it in and out of its case, and turn the sheet music. However, he can hold and play the instrument and use large-print music sheets.
South Lanarkshire refused the Pettigrews' request, claiming sufficient support was in place.
An additional support needs tribunal ruled it should not have denied Thomas the chance to participate.
The case, the first of its kind in Scotland, has been welcomed by human rights campaigners for establishing that inclusion should not "end with the school bell" and that extra-curricular activities are covered by equalities laws.
The Equality Act requires schools to make reasonable adjustments to avoid substantial disadvantage to any disabled pupil.
Due to additional support already provided by South Lanarkshire Council, Thomas has been able to take part fully in the school curriculum, and some extra-curricular activities such as a trip to the theatre.
In finding South Lanarkshire had unlawfully discriminated against Thomas because of his disability, the tribunal considered guidance issued by the Equality and Human Rights Commission on making reasonable adjustments for disabled pupils.
They found it had not met the duty to make reasonable adjustments and that Thomas was "substantially disadvantaged" from engaging in the club, adding: "His health and safety is compromised as a result. His additional support needs are not met.'
Iain Nisbet, head of education law at Govan Law Centre, which represented Thomas, said: "We are very pleased to have this early confirmation that a school's duties extend to after-school activities and that Thomas will now be able to take part in the guitar club.
"This ruling could not be more clear: the duty of inclusion for disabled pupils does not end when the bell rings at the end of the school day."
Thomas's mother, Catherine Pettigrew said, "Thomas has always been able to participate in mainstream education and school-related activities, just the same as other children, so he was very distressed when he couldn't participate in the guitar club – he felt that he was being left behind, that he was being excluded, which is very difficult for a 10-year-old.
"All he wanted to do was learn to play the guitar.
"It is important that Thomas can now learn to do something he loves, just like his friends, and also that other parents know that this type of support is available to them."
A spokesperson for South Lanarkshire Council said: "The council always strives to provide all the support that our young people need to participate fully in both curricular and extra-curricular activities. That includes strenuous efforts to ensure there is no 'substantial disadvantage' to disabled pupils.
"In this instance it was felt that the support provided was appropriate and offered a 'reasonable adjustment' that allowed Thomas to participate in the guitar club.
"The council is now reflecting on the findings of the tribunal and considering its position and legal options."