Quinn informed the EVO-STIK NPL First Division North club of his intention to stand down earlier this week following a ninth-placed finish to the 2016-17 campaign on Saturday after his side's 3-1 defeat at Clitheroe.
In a club statement announcing the departure of Quinn and his number two Lee Ashforth on Wednesday after their highest ever finish, officials at St Giles Road said they had "reluctantly" accepted his request after a "period of deliberation".
Quinn told fans he'd enjoyed "every minute" of his time at the club after taking them from the Northern Counties East League to the EVO-STIK NPL in 2014 as NCEL Premier Division champions.
Quinn, pictured, said: "It is the right time for me and the club that we go our separate ways. After gaining invaluable experience and leading the club out of the NCEL and establishing them as a top EVO-STIK side, it is now time for me to seek a new challenge in football.
"Brighouse gave me an unbelievable opportunity aged 27 and I have enjoyed every minute of my time at the club. I want to thank in particular the chairman and all the committee for their support along with all the players and supporters. I wish Brighouse every success in the future."
Brighouse Town chairman Charles Tolley said: "It is with great regret that we have accepted the resignation request of Paul but recognise and respect the reasons he has given for this decision.
"Brighouse Town Football Club is where it is today due in main to the contributions on and off the pitch that Paul has made. He goes with our blessing and best wishes."
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