The name of the Yarra Flats School was changed to Yarra Glen State School in September 1889 after the railway station opened and the town was re-named Yarra Glen. The school now had four classrooms and a dwelling for the head teacher. By the 1890s overcrowding required the head teacher to limit enrolments to 72 pupils. Further accommodation was not provided until the 1900s. Two octagonal shelter sheds were built in1908 and were being used as cloakrooms in 1910. The sloyd room (for woodwork) was added in 1911 it was converted to a classroom in 1953. The number of students had increased to 90 by 1953 and were occupying rooms which accommodated 56.

 In May 1954 a separate classroom and storeroom were built, the classroom being used for the infant classes. In 1957 a new classroom was added to the original building and used for Grades 5 and 6. The grounds were extended in 1915 with the purchase of an extra two acres and again in 1952 with the purchase of three acres from Mr and Mrs R. J. Lithgow.