The 49ers have endured two tough losses at the inside linebacker position this offseason, losing Patrick Willis and Chris Borland to retirement, but have confidence in up-and-comer Michael Wilhoite.
Wilhoite, 28, signed his exclusive rights free agent tender on Wednesday, according to a national report.
He is set to become a restricted free agent next offseason.
The homegrown linebacker out of Washburn University has been with San Francisco since 2011, but made his first start in 2013.
Wilhoite has been a force on special teams, and a valuable backup over the last two seasons at inside linebacker as the 49ers dealt with various injuries.
He has appeared in 32 games over the past two years, starting in 18 of them.
Wilhoite logged a full season in 2014 with NaVorro Bowman out of action, and recorded 87 tackles, six pass deflections, two interceptions and one forced fumble.
The 6-foot-0, 240-pound converted college safety expects to start alongside Bowman in the 2015 season.