A cornerstone of a boarding school such as St Anne's is its House system.  The girls, 85 % of whom are boarders, are comfortably accommodated in six boarding houses: Andrews, Frances Baines, Macrorie, Marianne Browne, Mollie Stone and Usherwood. A strong sense of competition exists between the Houses and regular interhouse competitions in Drama, Music and all sports take place.

Each House is cared for by a resident Housemistress.  She is the mother figure and liaises closely with parents. She is assisted in the House by resident staff and the senior girls. Junior girls are accommodated 3 or 4 to a room and senior girls have single rooms.  The well equipped House common rooms, each with its own television set and kitchen, are a focal point where the girls relax and socialise. Day girls are assigned to each house and are encouraged to be as much part of the House as the boarders are. Parents have the opportunity to meet each other at annual House get-togethers.