The Northern Irishman notified his players after the final game of the season, a 1-1 draw with Spartans on Sunday.
Kirk, and assistant Aaron Hughes, were hugely popular figures with Hearts Women’s team and were key in the side’s progress having taken over back in August.
Prior to his appointment as the women’s manager, Kirk worked with the first-team under Daniel Stendel and has had stints coaching the U15s, U17s, U20s and reserves sides.
“I’d like to thank everyone at Hearts for their support over the years and for the opportunities I’ve been given,” he told the club’s website.
“I’ve really enjoyed working with the women’s team over the past ten months. Like everyone, they’ve had such a challenging year but they’ve been an absolute credit to themselves and the club, and I’m proud to have been a part of their journey.”
Kirk now takes charge of a Brechin City side preparing for life in the Highland League.
The Glebe Park side recently appointed former Hearts boss Craig Levein as an advisor to the board.
Kirk told the Hearts players that the club will look to build on their progress going into the next SWPL1 season when it returns later this year.
The Tynecastle side are now looking for a replacement to carry on the excellent work of man affectionately known to many Hearts fans as ‘Ulster Andy’.
“Andy and his backroom team have worked tirelessly throughout the season and he goes with our best wishes,” sporting director Joe Savage said.
“The improvements in the side have been clear for all to see, so now we begin the search to bring in a new manager who can lead our Women’s First Team and Girl’s Academy into a new season and continue the upward trajectory.
“It’s a search I’m excited to be leading. The women’s game is booming and there will no doubt be a number of talented managers who would be eager to manage the Women’s First Team at a club of Hearts’ stature.”