This comes following an approach from Bury FC regarding their vacant managerial position over the weekend.
Bootle are currently sat in 9th place in the Pitching In NPL West Division table, having picked up nine points from their opening seven matches.
Former Warrington Rylands boss McNabb took charge of the Bucks back in March following the resignation of Ste McNulty.
He had previously spent time at Macclesfield, although his stint with the Silkmen lasted less than two months before he was forced to step down due to work commitments.
A Bootle club statement read: “The club would like to thank Dave for his contribution and wish him well for the future.
“The directors and committee will make a further announcement of next steps in due course.”
On Monday evening, Bury officially appointed McNabb as their new manager, with trusted assistant Tim Lees joining him at the NWCFL side.
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