St Brendan's School was first established in 1899 and conducted by the Sisters of Mercy.
The first school was erected at the west end of the Church and was registered by the Sisters of Mercy in 1906. The school was moved to the existing site, enlarged and opened in 1914.
In 1918 the Sisters of the Good Samaritan Order were asked to take over the Primary School from the Sisters of Mercy. At the beginning of the 1919 school year the Good Samaritan Sisters began their association with the school.
The modern St Brendan's School was built in 1958. Bishop O'Collins opened it. The Parish Priest at the time was Father J. Brophy.
In 1967 Bishop O'Collins blessed and opened the Science Laboratory, which now houses the Alvie and District Kindergarten.
The Secondary and Boarding sections of the school closed at the end of the 1970 academic year, due to the declining enrolment of the secondary section.
The involvement of the Good Samaritan Sisters in the school ended in 1989 and the first lay Principal Mr Neale Arthurson commenced in 1990. Sister Kathleen Spokes was the last principal from the Good Samaritan Sisters until 2002 when the Good Samaritan Sisters once again became involved when Sr. Veronica Quinn took on the responsibility of Principal.
A major refurbishment project was completed in 1997 which has seen a significant improvement in classroom, administration and toilet facilities.
In 2006 the Front Entrance, Administration and Principal's Office were remodelled.
In 2010 with the assistance of the Australian Government (BER) Program, all the classrooms and the Library were completely refurbished with new windows installed, new carpet, new desks and chairs and the interior repainted.
In 2012 a new Portable Classroom was relocated to the grounds as a specialist room, and is currently used for Art.
The old School Hall was refurbished in 2013 and a multipurpose area was created including board room, uniform shop and kitchen area to encourage cooking within the School curriculum.