Shams Charania of The Athletic and Stadium first reported Stojakovic is expected to step down from his role with the organization.
Stojakovic confirmed the news to Marc J. Spears of The Undefeated.
The Kings appear to be undergoing a significant makeover in their front office coming off their 14th consecutive losing season.
On Friday, The Athletic's Sam Amick reported Joe Dumars will be named interim vice president of basketball operations and assume general manager duties with Vlade Divac stepping down.
The Kings were included among the 22 teams to participate in the NBA season restart, but they lost five of their eight games to miss the postseason and finish the 2019-20 campaign with a 31-41 record.
Stojakovic has worked in Sacramento's front office since 2015, when he was hired as director of player personnel and development. The team promoted him to assistant general manager in May 2018.
Prior to his career as an executive, Stojakovic had a successful 13-year playing career in the NBA from 1999 to 2011. He spent eight years in a Kings uniform between 1999 and 2006 and won an NBA championship with the Dallas Mavericks in his final season.