The school building was inaugurated and blessed by Valerian Cardinal Gracias on 31 May 1960. Some of the Daughters of Mary Help of Christians, Auxilium Convent, with Rev Sister Superior, Bertha, attended the function held in the evening. There was a speech by the Cardinal followed by a few items of song and dance performed by the parishioners. The parish priest, Rev. Fr Theophilus Lobo, due to whose labours the building owed its existence, gave the concluding speech.

The school started as a co-educational school, initially with Stds I-III and students, mostly parish children. With a view to establishing a convent school at Bandra, the superiors had appointed two sisters from Auxilium Convent, Sr Zita and Sr Regina, to teach in the parish school at Pali Hill.

The new school opened its first academic year on 13 June 1960 with classes, Std. I, II, III (and lower and upper kindergartens which began functioning later). Half-day classes were held till the end of June, as the building was yet incomplete.

Initially St Anne's High School was run as day school but when admissions increased greatly, the school was run in shifts.

Following the inauguration of St. Anne's High School, every year new classes were added till the first batch of four SSC students appeared for the SSC Board Examination in 1966. The school secured cent percent results that year.

In Fr Trevor's initiatives included vocational guidance and counselling, the Scouts and Guides, and other extra curricular activities like field sports, elocution, dramatics, music and competitions, excursions and camps. American Peace Corp helpers who conducted classes in social values and ethics.

The newsletter was The Lion's Roar.

After Msgr Malcolm Mendonca became principal, the school building was raised, the present basement, the hall above, and the school office above the church extension, were built. Funds for the construction were collected by way of cultural programmes, fetes and raffles organised by the parish and the school. Msgr Malcolm Mendonca served until his transfer in 1982. Msgr Zachary D'souza took over as manager while Ms Greta Alvares continued as Headmistress. The school participated in inter-school competitions for elocution, science projects, teaching-aids exhibitions and sports events.

The school was made a center for S.S.C Maharashtra State Board Examinations. A laboratory and library were added.

Ms Congita Fernandes retired in 2002 after serving St. Anne's for 40 years.