Adam Schefter of ESPN reported the team will give Lynch a six-year deal.
Niners CEO Jed York issued a statement on the Lynch hire on Monday.
"During his 15 seasons as an NFL player, John epitomized what is so special about the game of football," York said. "A world-class competitor, his love and respect for the sport are unmatched, and you would be hard-pressed to find anyone in league circles who does not have great respect for his work ethic and passion.
"Having already helped lead a team to a Super Bowl title as a player, John is equipped with tremendous insight into what it takes to create a culture that breeds sustained success. Having spent the last eight seasons as an analyst with Fox, he has honed his skills as a talented communicator while also developing valuable relationships around the league and a vast knowledge of the NFL that will be beneficial to our team. As we learned more and more about John, it became apparent that he was not only one of the best to ever play this game but also a Hall of Fame caliber man, one who people are compelled to follow."
The 49ers have not yet officially hired a head coach, but according to Mike Silver of NFL.com, Atlanta Falcons offensive coordinator Kyle Shanahan is expected to land the job. The team cannot offer him the position until Atlanta's season ends, which will be after the Super Bowl. According to Schefter, the 49ers plan to offer a six-year deal to tie the combination together for the long term.
ESPN's Jim Trotter reported on Monday Lynch will have "final say" over the draft, free agency and 90-man roster while Shanahan will have say over their 53-man roster.
Matt Maiocco of CSNBayArea.com noted Lynch stayed at 49ers owner Jed York's house Thursday and flew with the team to meet with Shanahan in Atlanta.
Shanahan met with the 49ers on Friday, according to Eric Branch of the San Francisco Chronicle, along with potential general manager candidates George Paton and Terry McDonough, both of whom have the front-office experience Lynch lacks. The organization also interviewed ESPN's Louis Riddick, who also spent time as a scout.
However, Lynch got the job through what was a secret process, as NFL Network's Ian Rapoport described:
According to Schefter, Lynch called Shanahan directly and "volunteered for the job."
Shannon Sharpe of Fox Sports 1 apparently wants a job through the same means:
While Lynch lacks experience at this level, he is reportedly already set to hire help, per Pro Football Talk:
Interestingly, Lynch has been critical of Shanahan in the past, via John Middlekauff of 95.7 The Game:
Lynch played for Shanahan's father, Mike, for four years as a member of the Broncos.