The 59-year-old guided Serbia to two major tournaments in a row -- the 2022 World Cup in Qatar and forthcoming European championships -- for the first time.
As a result he will continue his work beyond Euro 2024 where Serbia's first match will be against England in Gelsenkirchen, Germany on June 16.
Group C rivals also include Slovenia and Denmark.
"The extension of our cooperation with coach Stojkovic is in line with FSS ambitions for the future," the federation said in a statement.
The former midfielder took over as Serbia coach in 2021.
As a player Stojkovic made 84 appearances for the former Yugoslavia between 1983 and 2001, and was one of the first top-tier European players to venture into Japanese football.
Stojkovic, nicknamed Piksi, spent eight years at J-League side Nagoya Grampus Eight.
After retiring as a player Stojkovic briefly served as chairman of Red Star Belgrade, before turning to coaching.
He returned to Nagoya as coach and between 2016 and 2020 was in charge of Chinese side Guangzhou.
