The 30-year-old was a regular for Fleetwood during the 2023/24 campaign, making 37 league starts following his move to the club last year. However, the club have issued their retained list and Heneghan is not among the players being kept on.
He will now be available to snap up as a free agent in the summer transfer window and it is difficult to imagine the defender not attracting EFL admirers.
Heneghan first arrived in Yorkshire in 2017, joining Chris Wilder at Sheffield United on the final day of the summer transfer window. However, despite having previously shone for Motherwell, he failed to break into the Blades side.
He turned in some promising displays under Darren Moore but saw his season with the club brought to a premature end by injury. Wednesday clinched promotion to the second tier in his absence and opted to release Heneghan following their Wembley triumph.
Fleetwood then handed him a deal but he will now seek pastures new. In a statement, Fleetwood said: "The club would like to thank all departing players for their efforts during their time at the club and wish them all the best for the future."