St. Mary's Sandakan, has the unique distinction of being the oldest school in Sabah. It began with the acquisition of 5 acres of land in Sandakan by Monsignor T. Jackson, the prefect Apostolic of the Mill Hill Order of Missionary Priest in May 1883. In July 24, 1883. Rev. Father. Prenger and Fr. Pundleider began the first school in Borneo, St. Mary's School.
The first pupils, 5 in all, were housed in a kajang hut. In February 1884, Fr. Pundleider left Sandakan to open up Bundu Mission. However, in November 1885, Fr. Prenger was ordered by Msgr. Jackson to leave because " Sandakan unhealthy, many Chinese sick, no good water and Fr. Prenger often ill."
The closure of the school was temporary. Rev. Fr. J. Byron, on his visit to Sandakan in July 1886, found 26 Catholics there. However, it was only a year later that Fr. Byron was able to re-establish the Mission and School in Sandakan. On August 15, 1887 Fr. Byron re-opened St. Mary's School, but only 1 boy turned up for registration. Untaunted, Fr. Byron continued his efforts. Slowly, the enrolment rose to 12. By 1888, a new building was built in order to cope with the rising student population.
The War years did not seem to have affected St. Mary's unduly and a major mile stone in the history of the school was reached with the appointment of Rev. Fr. A Stotter to the Rector of Sandakan in 1920. In 1923, he invited two De La Salle Brothers from Hong Hong to take over the running of St. Mary's School. Shortly after Fr. Stotter returned to Europe to attend the Chapter of his Congregation. On his return in1926, Fr. Stotter saw the need for a bigger school and a site was prepared. A new 3 storyed wooden building was completed in 1929. The ground floor comprised of classrooms; the first floor made up of class rooms and rooms for the priests. The third floor was mostly dormitory.
In 1927, Rev. Fr. B.J Davis came to Sandakan and and was put in charge of St. Mary's the following year. In 1931, he entered some candidates for the Hong Kong Local Exams, with great success. The following year he switched to the Cambridge Locals, also with success. St. Mary's became officially recognised as the centre for Cambridge Local Examinations.
However, war broke out in 1939 and North Borneo was under Japanese occupation from 1942 - 1945. It was in 1943 that the Japanese razed St. Mary's to the ground. There was neither Church or School standing. The period after the war belongs, rightly to, Rev. Fr. Anthony Moulders. He was visionary, architect, planner, contractor, all rolled in one, in the difficult process of reconstruction after the devastation of the war, and credit for putting St. Mary's back on its feet should be given to Fr. Moulders. On his arrival in Sandakan in 1952, he wasted no time in getting down to business. Through his tireless efforts, not only 1 school, but 2 schools were opened. In 1953, he built a 2 storyed 11 classroom school besides the church. But it was soon found to be too small and inadequate for the numerous students whose education had been disrupted by the war and who had a lot of studies to make up for.
In 1954, Rev. Fr.J.Van Haaren obtained a large piece of land at Mile 2 1/2, Labuk Road and he constructed a school to house the secondary school students while the previous school was turned over exclusively to the Primary school, being know as St. Mary's Primary School bandar (photo).
In 1991, Mr. Francis Tan took over as Headmaster. A catholic, he has done a lot in the beautification of the school and gave the school a facelift. Likewise in the field of academy, the school also excels in their annual UPSR examinations.
source - http://www.rc.net/malaysia/kotakinabalu/stmary/schools.htm