She believes the vertical grouping, where girls from all years belong to one home group throughout their time at school, is important to fostering the sense of whanau at such a large school.
When Mrs Baxter's resignation was initially announced she says many of the girls were worried she was leaving them to go to another school.
But she made it very clear she will not be doing this; she just simply felt it was her time to move on and create more time for herself and her family.
"I'm not resigning because I feel negative about anything, it's a very demanding job and along with that I'm a person who throws myself into things and that leaves little time of myself, family and personal life."
Mrs Baxter has always worked in education, teaching her first class at the age of 19.
She has had many jobs in the education field and started her teaching career at primary school before moving to secondary and tertiary education. She also had a stint teaching teachers how to teach.
Prior to taking on the role at girls' high she was deputy principal at Kavanagh College in Dunedin.
She says she has never felt the need to change occupation as she loves being around people and feels teaching provides really 'special moments'.
And there have been plenty of highlights during her time at Hamilton Girls' High School. However one that will have a special place in her heart was last year's centennial.
One moment during this event that was extremely special to Mary Anne was staff, old girls and old boys of Hamilton High coming together on the administration building balcony to watch the girls perform old school drills to Poi e and later the girls sang the school song with passion 'at the top of their lungs'.
Mrs Baxter says travel could be on the cards in the future and another job in the education field. She says she will definitely be returning to her home town Alexandra, possibly finding 'a warm home for the winter'.
Although Mrs Baxter leaves the school at the end of the year she says she is confident the students will carry on being wise young women, seizing new opportunities even without her leading the way.
"The girls are the heart of the school."