St. Mary's School was founded in the Parklands area of Nairobi in 1939 from Blackrock College in Dublin, Ireland. In September 1945, the school was moved to a temporary structure on an site on the land belonging to the St. Austin's Mission in the Muthangari area of Westlands. The present-day school buildings were completed in 1954, including the twin towers that stand at the school's quadrangle and the older St. Austin's Catholic Church, which sits beside the school's parking area. In between the towers is the staff room where teachers convene for meetings and take their breaks, which used to be the school's library.
From the outset, Saints has always had a combined primary and secondary school. Although only boys are admitted to the primary and secondary schools, girls are admitted to the International Baccalaureate diploma course which is a post-O-level programme offered by the school since 1982. Entrants are chosen on the basis of their KCSE and IGCSE results. The school year runs from January to November. The school is near its neighbouring sister school, Loreto Convent Msongari, separated only by a fence and a gate, and is situated about 1,000 metres away from rival Strathmore School. Students are encouraged to participate in extra curricular activities, which include sports, clubs, music and drama. All the school's sports teams are nicknamed "Saints", also the school's nickname.
Theatre
Since 1971, the school has been staging a musical every year, open to the general public. The musical week runs on specific dates from Tuesday to Saturday. The school has staged its own productions of famous plays such as The Mikado, The Yeomen of the Guard, The King and I, Joseph and the Amazing Technicolor Dreamcoat,The Sound of Music, Sarafina!, Cinderella, Oklahoma!, The Music Man, Ipi N'tombi, Aida, Zambezi Express, Amazing Grace . Notable guests who have attended the school's shows in the past include former Prime Minister of KenyaRaila Odinga.
Sports
Rugby
In line with its Irish origins, rugby is a central concern and a key activity designed to foment "spirit". Their rugby team won the Prescott Cup twice in a row but lost to Mang'u High School in the 2010 finals. They also host and have won the Blackrock Rugby Festival ten times and have been runners-up seven times, recently winning the 28th edition final, alongside many other cups. They also won the 2014 Nairobi county rugby championship against rivals Nairobi School at Upperhill school Nairobi, under head coach Thugana Riunga and Assistant coach Anthony Nyandigisi. However, the rugby team was relegated to Damu Pevu Cup from Prescott Cup in early 2015 due to poor performances in the 2014 Prescott season.
Football
is also a popular sport in the school, with honours in the recent past, such as the Keele Plate runner-up finish in 2010 and the Strathmore Under-11 Football Cup win for the under-11 team in 2008.
Swimming
Under the guidance of some of Kenya's coaches, the school has consistently produced strong swimmers who have dominated local competitions and gone further to represent Kenya in continental and international championships.