The former Richmond defender has worked at AFL House in the position of game analysis manager for the past two years and has spent this season on the MRP.
His departure is likely to be just the start of broader changes to the MRP and Tribunal system, which are expected to be finalised once this season concludes.
Bowden is joining AFL Northern Territory as community football – stakeholder engagement manager.
He'll relocate to Darwin with his wife Katie and four children in November.
"It's a wonderful opportunity to return home to the Territory and continue to be involved in the greatest game on earth," Bowden told AFL.com.au.
"I've always felt the pull to go back to the Territory and to contribute at an administrative level and give something back to the game that has given me a great opportunity in spending almost two decades in Melbourne."
Bowden will remain on the MRP up until, and including, the grand final, along with chairman Mark Fraser and former racing steward Des Gleeson.
