SANTA CLARA, Calif. >> The San Francisco 49ers officially hired Atlanta offensive coordinator Kyle Shanahan as their new head coach on Monday, more than a month after firing Chip Kelly after just one season.

The 49ers settled on Shanahan a couple weeks ago but had to wait until after the Falcons played in the Super Bowl to sign him to a contract. Shanahan will be formally introduced at a news conference later this week.

Shanahan is the son of two-time Super Bowl winning head coach Mike Shanahan, who also won a title as offensive coordinator in San Francisco in 1994. The younger Shanahan served as a ball boy then but now will be tasked along with new general manager John Lynch with rebuilding a team that just matched the worst record in franchise history with a 2-14 mark, leading to the dismissal of Kelly and general manager Trent Baalke.

“As a young man, I had the unique benefit of being exposed to the storied history of the San Francisco 49ers firsthand,” Shanahan said in a statement. “From that exposure, I developed great respect for those who created a world-class, championship standard. As this team begins the task of re-establishing that standard, I could not ask for a better partner than John Lynch. He is a man who certainly has personal knowledge of what championship organizations look like. John and I look forward to establishing a strong culture that will serve as our foundation for constructing this team.”

Shanahan won the AP award as the top assistant coach in the NFL this season when he helped the Falcons post a league-high 33.8 points per game in the regular season and return to the Super Bowl for the second time in franchise history.

That ended in disappointment after Atlanta blew a 28-3 lead to New England and lost 34-28 in overtime. Shanahan came under criticism for his play-calling in the fourth quarter.

He called a deep drop back on a third-and-1 that led to a sack and fumble that sparked the Patriots comeback and then with Atlanta in field-goal range to make it a two-possession game late, Shanahan again passed up on the opportunity to run, leading to a sack and a holding penalty.

Those were rare blots on an otherwise stellar season as a play-caller that led Lynch to call him the “catch” of the head coaching cycle. San Francisco was the last of six teams to hire a coach this offseason.

“As an offensive mind, I think he stands alone in the National Football League, as evidenced by the explosive and record-setting offense in Atlanta,” Lynch said. “Though he grew up around coaching, what has most impressed me about Kyle is that he’s become his own man in the profession. Our philosophies on football and our visions for leading the 49ers back to being a championship team align in every way. I am thrilled to have Kyle Shanahan on board.”

The 37-year-old Shanahan becomes the third youngest coach in franchise history. Jack Christiansen was 34 when he was hired in 1963 and Frankie Albert was 36 when he coached his first game in 1956.

Shanahan got his first NFL job as an offensive quality control coach in Tampa Bay in 2004. He also served as an offensive coordinator in Houston, Washington and Cleveland before arriving in Atlanta last season.

It was clear that Shanahan was the choice for the 49ers when he was the only candidate to get a second interview and the team hired Lynch as general manager after a recommendation from Shanahan.

“Throughout this process, we learned many things about Kyle that convinced us he is the perfect coach to lead this team,” CEO Jed York said. “Over the years, he has proven to be one of the brightest minds in the game of football and his recent success speaks for itself. Kyle’s leadership has brought the best out of his players at every phase of his career and we look forward to watching him build a talented staff to accomplish the same with our players.”

After making three straight trips to the NFC title game and one Super Bowl appearance under coach Jim Harbaugh from 2011-13, the Niners’ fortunes have fallen in recent years.

Harbaugh was let go after an 8-8 season in 2014 in part because of conflicts with Baalke and then Jim Tomsula and Kelly each had one-year tenures as coach.