The Vanarama National League North side say he leaves on good terms after confirming their status in the division for another season.
Wilcox joined the club in January last year when they were rooted to the bottom of the table having won just once in 13 games.
He saved them that season and confirmed their status once more at the end of the season just gone.
This season also saw Farsley progress to the quarter final stage of the FA Trophy.
In a lengthy statement released from the LMA, Wilcox said it was time for 'a new chapter' before thanking people involved with the club for their help.
A statement on the club's website confirmed Wilcox's departure. It reads: "Russ came into the club at a difficult time and was the pivotal figure in keeping the club in the National League in his first season.
"Last season saw an exciting run in the FA Trophy and some great performances in the league that ultimately ended in us securing our National League North status again.
"As ever, there will be multiple rumours surrounding the reasons behind Russ’s departure, but the club can confirm that there has been no fallout or disagreements.
"Russ leaves the club with the best wishes of the board and thanks for his efforts and professionalism, and he will always be welcome at The Citadel.
"We wish him every success in the next step of his journey!"