The team hopes to acquire a sixth or seventh-round pick for Wilhoite, the report says.
Wilhoite, an undrafted free agent out of Division II Washburn in 2011, started 16 games last season, recording 87 tackles and two sacks.
The 28-year-old is expected to have his role reduced this season with Patrick Willis and NaVorro Bowman returning from injuries.
From the report:
Wilhoite, who entered the league in 2011 as an undrafted rookie from Washburn University, is a pending exclusive rights free agent. That means he is not under contract with the 49ers for 2015 but cannot negotiate with any other teams. The 49ers can tender him at a minimal salary, then trade his rights.
San Francisco went 8-8 and finished in third place in the NFC West last season.