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Currently the schooling of pupils is through affiliations by choice of SSC of MSBSHSE, Pune and ICSE of Council for the Indian School Certificate Examinations, New Delhi.
For admission to the FCRIT, prospective candidates from the native state of Maharashtra need to pass their Higher Secondary (School) Certificate / Standard XII examination of the Maharashtra State Board of Secondary and Higher Secondary Education or its equivalent from CBSE or CISCE.
The school is the only one in the region following the X-std ICSE and XII-std CISCE's national curriculum.
Started by missionaries of the Convent of Jesus and Mary in 1912, St. Agnes High School initially housed two different schools — one affiliated to the Council for the Indian School Certificate Examinations and the other to the Maharashtra State Board.