The ex-Hearts and Hibs No.2 took over the role in the summer when former manager Gary Locke left to return to Tynecastle as a club ambassador.
Brown’s decision has come off the back of Saturday’s 1-0 defeat away to Berwick Rangers, a result which kept the Blue Brazil bottom of the League Two table.
The club had managed to score only once in their last 10 games in all competitions, which came from the penalty spot in a 1-1 draw against Clyde. They’ve yet to win since a 1-0 victory over Edinburgh City on the second weekend of the season.
Brown thanked Cowdenbeath officials and staff for their efforts during his time at the club in a statement released on the club website.
He said: “I really hadn’t envisaged going back into management when I came to Central Park. Gary Locke asked me to help him and I was delighted to do so. I was enjoying just being back in the game. Then, when Gary left, the club asked me to step in and I agreed to do so.
“It’s fair to say it has been a real challenge with rebuilding to be done and of course we have had to rely heavily on young players. Results haven’t gone our way so far with so many narrow 1-0 defeats. We showed improvement down at Berwick though and there is something there I believe to build on.
“To be absolutely honest I just wasn’t really enjoying being back at the sharp end. I think leaving now gives someone else an opportunity to give it a go and also time as we are only 10 games into the season.
“I would genuinely like to say though that they are great people at Central Park and I do wish the players, fans, staff and board all the very best for the future.
Chairman Donald Findlay said: “It has been a pleasure working with Billy and to witness his real enthusiasm for the game. Unfortunately results and indeed goals have been hard to come by, but it is typical of Billy that he willingly came in to help us last season and then stepped in to help us further when Gary left.
“He has worked tirelessly in his time as manager at Central Park. Now he has intimated his desire to stand down in an open and straightforward manner allowing us time to seek his successor.
“Billy leaves us with my own personal sincere thanks for his service to Cowdenbeath FC and the very best wishes of all the board.”