The former England Under-20s and London Wasps winger will depart Rudding Lane following six years at the club, during which time he has also spent a period of time acting as the Aces' commercial chairman.
"I have absolutely loved my six years at the club," 35-year-old Doherty said.
"I have always tried to leave my shirt or role at the club in a better place.
"We now have a long-lease on our land and have a sustainable business model, with our junior academy at the heart of what we do. This has already started to bear fruit with a huge number of players transitioning into 1st XV and senior rugby.
"Planning is well on the way for our ground redevelopment and the club can kick-on to future success, as we have created solid foundations.
"I would sincerely like to thank all the players, coaches and members who have supported me at the club during my time."
Doherty joined Harrogate for the 2016/17 season following the club's move from their old Claro Road base to Rudding Lane, at a time when budgetary constraints were significant.
A number of senior players moved on, leading to an inexperienced Aces side being relegated from National Two North in the final game of that season.
Doherty rebuilt the senior squad in the seasons that followed and eventually secured promotion back to National Two North at the end of the Covid-19-affected 2019/20 campaign.
The former Barbarian also established the HRUFC Academy, with a number of graduates making their senior 1st XV debuts this year, creating a lasting legacy for his time at the club.
'Gate, who currently sit bottom of National Two North but are not in danger of relegation due a restructuring of the leagues, are now reviewing their options as they begin a search for Doherty's replacement. The club say that they intend to have an appointment lined up before the end of the season.