McCartney, who has spent 11 seasons at Skilled Stadium in a development and coaching role, will next year be an assistant coach with the Bombers.
Geelong football manager Neil Balme said his club hoped McCartney, seen as pivotal in developing many of the club's younger players on the way to the Cats recent successful era, would continue in his role but understood him wanting to play a role in the coaches' box.
"It was in the club’s plans for Brendan to become a development coach who would solely focus on developing our younger players, however he has now informed us he is looking to pursue a senior match-day role instead," Balme said.
"On this basis we have reluctantly accepted Brendan’s decision to resign."
McCartney's departure from Geelong may fuel speculation former senior Cats coach Mark Thompson could join the Bombers in a coaching capacity next season.
Many believe Thompson, who stepped down from the top job at Geelong earlier this month, may yet return to his former club to assist Hird.
Essendon's coaching staff has undergone massive changes since Hird was appointed to the senior position.
McCartney joins Sean Wellman and Simon Goodwin as assistants on a coaching panel that no longer has any remnant of the Matthew Knights era.
Former assistants Alan Richardson, Gary O'Donnell, Scott Camporeale and Ashley Prescott have all departed, with Essendon's general manager of football operations Paul Hamilton confirming on Tuesday that Adrian Hickmott had also joined the exodus.
Hamilton said the club was delighted to secure someone with McCartney's coaching and development experience.
"Brendan will be a really important part of our coaching team going forward and we are really excited about the contribution we know he will be able to make," Hamilton said.
"We have been clear in our ambition to put together the best possible coaching group to support our new senior coach James Hird and this is another step towards that. Brendan knows football back to front and more importantly, the underlying trends for where the game is going.
"He is also a great manager of people and players and comes highly regarded for his development of players and his ability to teach.
"While his role will primarily be working with our AFL side, we believe Brendan will be able to pass on some valuable knowledge to our development academy as well."
