He replaces Nick Montgomery, who has taken the reins at Scottish club Hibernian after his stunning fairytale success with the Mariners.
Jackson's most recent appointment was a stint at MK Dons, where he lasted less than six months after they were relegated to League Two.
But he previously spent a significant amount of time at Leeds United, predominantly working in their academy and U23 set-ups.
The Mariners said in their statement Montgomery had endorsed Jackson's appointment.
"With the departure of Monty and (assistant) Sergio (Raimundo), the search for replacement leadership has taken centre stage," Mariners chairman Richard Peil said.
"While we had a substantial number of applications from people around the world, Mark immediately showed that he is the perfect fit for our club
"Having spent several seasons in youth development at Leeds United, many of which were under a world class coach in Marcelo Bielsa, and with our focus on youth development, it was a no brainer when Mark put his hand up for the role.
"Mark will fit seamlessly into the community and is a great cultural fit for us as a club."
The former Leeds United and Scunthorpe defender was determined to maintain the Mariners' focus on bringing through young players.
"I want to play front-foot football and dominate every part of the game," Jackson said.
"That is my philosophy, that is how I want my teams to play, and that is what I will bring to the Central Coast.
"The club is in a fantastic position, so I want to continue that good work and help the club grow and continue to move forward."
The Mariners kick off their title defence away to Adelaide United at Coopers Stadium on October 20.
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