Thomas, 23, was drafted third overall by San Francisco in 2017. He totaled 31 tackles in 13 starts last season and has accumulated four sacks throughout his two years in the league.
San Francisco holds the No. 2 overall pick in Thursday's NFL draft, where it's been speculated the club could select defensive end Nick Bosa.
The 49ers have been active this offseason, most notably acquiring pass-rusher Dee Ford from the Kansas City Chiefs for a 2020 second-round pick.