Ronan Bass has been principal since 2018, but Selwyn Times understands he has been on leave since the start of the school year.
Deputy Antony French has been the acting principal.
College board chair Vanessa-Amy Greenwood said Bass resigned earlier this month and was on leave until the end of the year.
"At the moment, Antony is still acting principal and we’ll be going through the recruiting process shortly."
Greenwood would not say why Bass resigned or if he was on paid leave.
Bass did not respond to calls from Selwyn Times.
She said the board would be going through a "rigorous" process to find a replacement.
"We need to find the right fit for the community."
Ellesmere College-Te Kāreti o Waihora is a co-educational high school in Leeston for students in years 7-13. Based on Leeston Dunsandel Rd, it has a roll of about 500.
- A previous version of this story contained a photo incorrectly identified as Vanessa-Amy Greenwood. We apologise for the error
