The 49ers acquired Boldin from the Baltimore Ravens last March for a sixth-round pick.
Boldin had a huge season for the 49ers, a season after beating them in the Super Bowl. The 33-year-old had 85 catches for 1,178 yards and seven touchdowns.
Boldin saved the 49ers' offense for the first 11 games when Michael Crabtree was out with a torn Achilles.
He was a leader of the team and respected by coaches and players. Both San Francisco general manager Trent Baalke and coach Jim Harbaugh said keeping Boldin was important. Boldin indicated after the season he wanted to remain with the 49ers.
ESPN.com 49ers reporter Bill Williamson contributed to this report.