Stajcic took over as a caretaker at the A-League struggler in March, having previously coached Australia's women's team, the Matildas.
The 45 year-old oversaw improvement in Gosford, with two of the Mariners' three wins for the season coming in the six games Stajcic coached.
Central Coast – the 2013 champion which has finished bottom the past two seasons – named Stajcic its coach until the end of 2021-2022.
"I would like to thank the Central Coast Mariners for inviting me to this great club. It's been an absolute privilege being the caretaker coach of this team," he said. "For us to become a successful club again, we need the support of the whole community and we need to show mental toughness and resilience to once again become the proud symbol of the Central Coast.
"I'll never forget walking through the doors on day one. To feel the welcoming aspect of the club, the warmth from the people within the club, to see the hard-working people behind the scenes, it really was eye opening to see how much these people love the club, how much passion there was.
"Now that I know that I am going to be here for the next three years we really need to set our mind on building this club. We all know that it's been a tough few years and nostalgically we look back to the glory days, but we need to reflect on the past few years and think about how we can rebuild."