Mr Coe will be moving north to become headmaster of Napier Boys’ High School, the school said in a statement.
Board co-chair Chami Abeysinghe said Mr Coe was leaving the school in a strong position.
Since joining the school in 2017, he had raised academic standards and led improvements including classroom upgrades and new heating systems.
"Simon leaves a great legacy. Successful, well-rounded young men graduate from Southland Boys’ High School with the skills they need to succeed in life."
Mr Coe said he was "hugely proud" of the school and its place in the community.
"The school has a strong sense of identity and rightly stands tall within the Southland community - where its students wear the school crest with pride.
"The rewards of being involved in a busy and active boys’ school are immense.
"Seeing the boys succeed where they thought they couldn’t, pushing their own boundaries and taking advantage of opportunities presented to them is something I am very proud of."
