St. Michael's Secondary School is a dual-session English secondary school in Sandakan, on the east coast of Sabah, East Malaysia. It is situated on a 20-acre piece of land on Elton Hill. The school, founded by Rev. William Henry Elton in 1888, is one of the oldest schools in Sandakan.

St. Michael's Secondary School started with only one student when it opened on October 5, 1888. In the first two months, Rev. William Henry Elton taught this student English while learning Malay and Chinese languages from him. From the third month, the number of students gradually increased. From 1901 to 1913, Mr. Alan H. Elton, the son of Rev. William Henry Elton, was the Headmaster of St. Michael's School. By 1910, there were two Chinese teachers, Mr. Leong Fah Kyam and Mr. Fong Chung Fui.

By 1920, there were 80 students, 36 of whom were boarders, under the charge of Principal Currey and two teachers - Chong En Siong and Lim Siong Teck. In the same year, the first boy scout troop was formed by Rev. T. Cecil. In 1927, there were three teachers, and they were Mr. Koo Pui Shin, Mr. Simon Chong Yew and Mr. Chin Vu Sang.

In 1928, there were over 100 students, 52 boarders and four teachers. Between 1928 and 1945, the Principals included Mr. W.T. Keble, Rev. S.M. Collier, Mr. B. J. Sole, Rev. J. Paisley, Rev. H. Cutler, Rev. Henthorne, Rev. P. Howes, and Dr. Dennis Brown.

By 1934, there were 131 students and 42 boarders. In December that year, nine boys sat for the Cambridge Preliminary Examination, and six of them were successful. in December 1936, one boy sat for the Cambridge Junior Examination and was successful.

After the Second World War, St. Michael’s School was rebuilt and opened in 1946 as a primary-secondary school, housed in a simple structure, dubbed the Cattle Shed. Mr. Fu Yun Fatt was the Principal. Upon the arrival of Mr. Kenneth D. Franklin as Principal of the school in 1951, the school began to grow rapidly both in size and space. He endured to extend the school from Form 2 through the Cambridge Overseas Junior School Certificate to the Cambridge Overseas Senior School Certificate level by 1953, when the school produced the first three Cambridge Overseas Senior School Certificate recipients, namely Thien Thau Khiong, Hiew Vui Khiong, and Fu Yin Henn. The Cattle Shed was replaced with a two-storey building in 1953. A tuck-shop and the Principal’s residence were built nearby, with the boarding house below the hill.

Developments continued with the arrival of Mr. John Brummell as Principal in 1956. With the establishment of St. Gabriel’s Primary School, St. Michael’s School became a full-fledged English secondary school, and it was renamed St. Michael's Secondary School, with students in classes ranging from Bridge Class to Form V.

In March 2017, Mr. Henley Liew Yun Ye returned to St. Michael’s as the school Principal for another term. The school enrollment was about 1,100. Owing to constraints of space and facilities, Mr. Liew began to reduce the enrollment to 1,000 in 2018, and , by 2019, the total student population was 910.

Today, there are two multi-storey buildings in the St. Michael’s Secondary School compound. One of the buildings is a 2-storey wooden structure consisting of classrooms, a school hall, a cafeteria, and a utility room. The other is a 5-storey concrete building that houses four laboratories, the staffroom, the principal's office, a library, an auditorium, two workshops, a kitchen, an art centre, a dental clinic, a bookstore, and a sports store.