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Principal Linda Miller said other than for a few months in 1979, this was the first time the school had introduced a house system.
The school is 143 years old.
After consultation with pupils, staff and alumni, it was decided the houses would be named after ex-pupils - Allan (orange), Benjamin (blue), Cruickshank (red) and Williams (green).
Allan House is named after Flora Allan, dux of Otago Girls' High School in 1879 and principal of the school from 1912-21.
She attended the school from 1876 to 1879.
Benjamin House is named after Ethel Benjamin, New Zealand's first woman law graduate (1897) and the first woman in the British Empire to appear as counsel in court.
She started at Otago Girls' in 1883 when she was 8 years old and was a pupil at the school until 1892.
Cruickshank House was named after Dr Margaret Cruickshank, New Zealand's first woman to be registered as a doctor.
She was a pupil at the school from 1888 to 1891 and dux in her final year.
Williams House was named after Yvette Williams (now Corlett), the first New Zealand woman to win an Olympic gold medal.
She won gold in the long jump at the Helsinki Olympics in 1952, and was a pupil from 1942-45.
Siedeberg was also an obvious choice, but was not considered because a building at the school is already named after Emily Siedeberg, New Zealand's first woman medical graduate.
Pupils and staff were recently notified what house they would be in, and Phoebe Morrison (green), Melanie Paddon (orange), Katie Borich (red) and Alex Lesa (blue) were named house captains.
The four gave a presentation on their house namesakes at a recent special assembly, where they were presented with house leader and prefect badges.
Ms Miller said the house system was established in a bid to build on the history and tradition of the school, and to showcase some of its ex-girls, their qualities and their dispositions.
''Where you have house systems, research shows there is greater interaction between pupils and staff, and it builds spirit within the school.
''It's a way of providing additional support for girls in the school and a way of introducing a fun but competitive environment,'' she said.