Jackson, who was contracted for two more campaigns, will leave the Mariners to take up a yet-to-be-revealed international coaching opportunity.
Friday's news comes just nine days before Central Coast get their season underway against Newcastle on October 19.
Jackson joined the Mariners ahead of the 2023/24 ALM season, guiding them to both the Premiers Plate and Championship trophy, as well as the AFC Cup title in what was a historic treble.
Central Coast will now begin the process of appointing a new head coach.
In the meantime, assistant coaches will lead the team for training and in Sunday's Fan Day trial match.
The club say an interim may be appointed to guide the squad while the search for the next head coach continues.
"While Mark's decision has come as a surprise, the club remains resolute and strong, and our players are professional athletes who are preparing as normal as we move toward our exciting clash in the F3 Derby against our fierce rivals, the Jets," Central Coast said in a statement.
Last month, reports emerged that the rumoured appointment of Sydney Olympic coach Labinot Haliti at the Mariners in a director of football role had created a power struggle with Jackson.
Central Coast, who are experiencing ownership issues, were also forced to explain to Professional Footballers Australia why player payments had been late last month.
Just under a year ago, Rich Peil quit as owner, citing the A-League's funding cuts as a major reason behind his decision, handing the reins back to previous owner Mike Charlesworth.
Shrinking revenues mean clubs have been feeling the pinch.
Western United were placed into liquidation in August, and will effectively be in a state of hibernation for this season while they fight for survival.
Central Coast were already being tipped to finish near the bottom of the ladder this season, and Jackson's shock exit will make things even tougher.
Mariners chief executive Greg Brownlow thanked 48-year-old for his exceptional contribution to the club.
"We are grateful to Mark for the commitment he's shown during his time at the Mariners," Brownlow said in a statement.
"He's led the team with great passion and care for our players, and we wish him all the best for his next challenge internationally."
Meanwhile, wooden spoon favourites Perth Glory have signed former Welsh international Tom Lawrence on a one-year deal.
The 31-year-old forward started his career at Manchester United, where he made one first-team appearance, before spending time at Leicester City, Glasgow Rangers, Ipswich Town, Cardiff City, Blackburn Rovers and Derby County.
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