Brown, 36, was given his first managerial role by the Cod Army in May 2022 having called time on his playing career earlier that month.
He managed 19 wins and 21 draws in 64 games in charge, but a poor start to this campaign has brought an end to his tenure.
"We worked hard throughout our time at the club, after a challenging start, to continue the club’s excellent record in League One. I was fully committed to the club and was excited to sign a new contract in the summer, with ambitions to build on our 13th place finish last season and record-breaking FA Cup run.
"I would like to thank Steven, Barry and Owain Fôn Williams for their support and hard work on and off the pitch. I would also like to thank the wider staff team at the club, who show up every day to make sure the team can perform to the highest possible level.
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