Bourke's departure will bring an end to his five-year tenure with the team.
Canterbury Rugby will start searching for a new head coach following the NPC season.
Bourke joined Canterbury as assistant coach in 2021, before stepping up to become head coach in 2022.
Bourke said resigning from the role was the "toughest decision" of his career but he is still firmly focused on the season ahead.
"It has been the biggest privilege of my rugby journey to coach this team and to represent a province with such an incredible history," Bourke said.
"I’m really proud of what we’ve been able to create together, and any successes have come down to the collective effort, hard work and support from everyone in and around our environment.
"This has been the toughest decision of my career because of the strong bonds and connections I feel towards the region but I feel now is the right moment for someone else to step in and take the team forward into the future.
"My absolute priority is this NPC season and doing all we can to finish on a high.
"I’ll always be honoured to have been part of the Red and Black family, and to the fans, players, staff and community - thank you for making these years so special and making me a better person."
He then took up a coaching role at Rugby United New York before returning to New Zealand to join Canterbury.
He took the red and blacks to the NPC final in his first season as head coach. Bourke joined the Chiefs as an assistant coach in 2023 and is also part of the New Zealand under-20s coaching team.
Canterbury Rugby chief executive Tony Smail said Bourke will "leave behind a legacy that will be part of this organisation for years to come".
"During this time, he has brought energy, leadership, and a genuine passion for the game, while showing an unwavering commitment to the growth of rugby and players across the region," Smail said in a statement.
"Marty has played a pivotal part in shaping the team’s culture, driving performance standards, and inspiring the next generation of Red and Black talent. His influence will be felt well beyond his tenure.
"Marty has poured his heart into this team and this province.
"He’s been a huge part of Canterbury Rugby, community and high-performance rugby, driving standards and developing players who love wearing the red and black as well as those who aspire to.
"His leadership, professionalism, and influence has been felt right across our organisation, and he leaves behind a legacy that will be part of this organisation for years to come.
"We look forward to seeing where his coaching journey takes him next and thank him for the passion, commitment and care he has shown for Canterbury Rugby.
Smail said Canterbury Rugby will confirm the 2026 coaching group after the NPC season, with the search for a new head coach set to begin once reviews are complete.
-Allied Media
