The 26-year-old shot-stopper spent the second half of the season on loan from Portuguese outfit Sporting at the DW Stadium.
Stojkovic made four Premier League appearances under Roberto Martinez and thoroughly enjoyed his time in England.
He is set to play a key role for his country in this summer's World Cup finals and insists nothing will be completed until after the tournament.
The former Nantes keeper cost Sporting €2million (£1.68m) in 2007 and are believed to want around €800,000 (£675k) for his transfer.
"Wigan are negotiating with Sporting and I don't believe there will be a problem reach a deal," said Stojkovic.
"My desire is to stay in the Premier League, but this will only become official after the World Cup.
"I spent six months with Wigan and I think their manager (Martinez) is interested in me.
"This is good news because English football has really impacted me. It's really incredible.
"I knew from my first day as Wigan that I'd do a job for the club."