The announcement by San Francisco came via a Twitter post by CEO of the team Jed York, who with Trent Balke the team’s general manager, met last week with Kelly in New York.
The Philadelphia Eagles fired Kelly, who is 52, with one game remaining in the regular season. The Eagles ended the season 7-9 but were 10-6 for two straight seasons before this year.
Prior to becoming a head coach in the NFL, Kelly had a highly successful career at the college level starting at the University of New Hampshire and then moving over to the University of Oregon.
His teams have always been known for their fast-paced, high-powered offense, something San Francisco must improve after the team finished next to last in scoring during the 2015 season.
The offenses for the Eagles under Kelly ranked in 2013 and 2014 in the top 5 in the league, but slipped to No. 12 in 2015. On the defensive side, the Eagles for the past three seasons were No. 29, No, 28 and No. 30, with certain players complaining the pace of the offense under Kelly meant the defense ended up on the field too often and too long.
Philadelphia was dead last in time of possession this past season in the NFL.
Eagles pass rusher Connor Barwin said he felt bad for Billy Davis his defensive coordinator because the numbers were skewed. Barwin said that the defense played three games more than did Seattle and were not as bad as many of the numbers looked.
Other players had complained that Kelly was too hard on them, as he only knew how to coach college players and not professional athletes.
Kelly knew Tom Gamble, the senior personnel executive with the 49ers, as he was part of the front office with the Eagles during 2013-14.
Gamble is believed to be the person to encourage the 49ers to make the initial interview and assuaged officials with the 49ers they could work with Kelly.
Kelly was awarded the head of football operations with the Eagles following a power struggle with the front office before last season.
However, he was highly criticized for making certain personnel moves like trading LeSean McCoy an All-Pro at running back and sending Nick Foles a quarterback to St Louis for quarterback Sam Bradford.