School of the Holy Spirit was set up by Bishop Birch 1976 in one room in Seville Lodge, Callan Road catering for three students with Emotional Disturbance and Behavioural Difficulties, and with a complement of one teacher. The first principal of the school was Mrs. Orla Hickey.

By 1990 The numbers of students from Kilkenny city and county continued to increase. At this time there was a staff of two teachers and two voluntary workers working in the school. In 1992 Mrs. June Barrett was appointed principal. 

By 1994 the growing school community moved to a refurbished premises on Gaol Road. The numbers of students and staff continued to grow.

By 1996 a number of students attending the school were assessed with Autistic Spectrum Disorder. In response to this appropriate training was resourced for staff and specific programmes put in place for the students. TEACCH, Structured Teaching, Picture Exchange Communication System and Sensory Integration programmes were introduced into the school to meet the needs of the students. Students also received Music Therapy.

It was recognised that a new purpose built school was required in order to accommodate the growth and development of School of the Holy Spirit. It was envisaged that such a building would have to be purpose built in order to provide the optimal educational and therapeutic environment for the academic, personal and social development of the students of the school.

On 30th June 2008 Bishop Seamus Freeman formally laid the foundation stone at Seville Lodge for the new school.

28th August 2009 a new purpose built state of the art School of the Holy Spirit opened its doors to the school community.

This new building, funded by the Department of Education and Skills provided the students with 13 classroom units (classroom, quiet room and bathroom) and several individual tuition rooms.
Sensory rooms, Snoezelen Rooms, Art and Woodwork room, Home Economics room Library, PE hall and Hygiene suite are also part of the school.

Play and recreation facilities include a Sensory Garden, ball court and an Autism Specific playground. Stone Developments, a local company were instrumental in providing our uniquely designed Keyhole Sensory Garden.

In 2011 Mrs. Karen Lowther was appointed principal, the school continued to grow, and secondary education provision was established and developed to include Junior Certificate and Leaving Certificate Applied. 
In summer of 2022 Mrs. Ann-Marie Butler was appointed principal and took up her position on September 1st.