Flores was signed to a five-year deal, a source told ESPN's Adam Schefter. Of the eight new head coaches hired this winter in the NFL, Flores was the only one to receive five fully guaranteed years, according to the source.
Other head coach deals were mainly four years and included a team option for a fifth.
Dolphins general manager Chris Grier, in charge of his first coaching search, sought someone with similar beliefs of how to build a contender.
He decided on Flores, the 37-year-old Patriots de facto defensive coordinator who started his career the same way as Grier -- as a New England scout. That Patriots connection likely played a significant role as the Dolphins seek a way to dethrone their longtime rival.
"To be a head coach in this league is a dream come true, to be head coach of the Miami Dolphins is a dream come true. This is a great organization with a great history, with a great fan base and I'm excited to be here."— Miami Dolphins (@MiamiDolphins) February 4, 2019
We go one-on-one with Head Coach Brian Flores pic.twitter.com/R7EmdEhbB9
Flores was the first person the Dolphins interviewed after they fired coach Adam Gase on Dec. 31. The New York Jets hired Gase as head coach 12 days later. The Dolphins decided on Jan. 11 to offer the job to Flores but had to wait until New England's season ended to complete an agreement.
"I wasn't in a rush to become a head coach," Flores said. "I had a good job in New England."
While preparing for the Super Bowl, Flores also began to hire a Miami staff. The group is expected to include former Colts and Lions head coach Jim Caldwell as assistant head coach, Patriots receivers coach Chad O'Shea as offensive coordinator and Packers assistant Patrick Graham as defensive coordinator.
"Two things that stand out immediately when you meet Brian are his football intelligence and leadership skills," Grier said in a statement. "Brian is widely respected throughout the NFL. He paid his dues in New England working in personnel, on offense, defense and special teams, which helped him build a great understanding of what it takes to win.
"If you talk with anyone who has played for him or worked with him, you will hear about his ability to lead and get the most out of people. Brian sets a high standard for his players and coaches and we are completely aligned with our vision on how to build a successful organization."
Flores is also the first full-time minority coach in franchise history and one of four minority coaches currently in the NFL.
Flores takes over a team that seems headed for somewhat of a rebuild, as owner Stephen Ross alluded to after firing Gase.
"We're going to look to really build this organization based on our needs and if it takes a year or so -- two years, three years -- we are going to be there." Ross said.
That means Flores is expected to get the time needed to overhaul the Dolphins' roster and culture to build a true contender. That will start with a decision at quarterback, as Ryan Tannehill's future is in peril. Grier said a decision on Tannehill's future hasn't been made yet and they haven't ruled out selecting a quarterback in the draft.
Flores is braced for the frustrations that come with rebuilding.
"That's part of leadership -- dealing with adversity," he said. "There's going to be some pain. There's pain for every team."
As for his curtailed Super Bowl celebration, he wasn't complaining.
"No, this is not getting cheated at all," Flores said. "That was a great experience, but I guess I've always been this way -- I look forward."
Flores has coached offense, defense and special teams, along with a stint serving as a scout in New England. He had spent his entire coaching career -- since 2004 -- with the Patriots. He will have to defy the lack of success that has followed many Bill Belichick assistants when they leave for another head job.
Flores is the Dolphins' 10th head coach (including interims) since 2004, and he will have to do what none of the others could -- lead the Dolphins out of mediocrity. Miami finished between 6-10 and 10-6 in each of the past 10 seasons, the only team in the NFL to do that. It went 7-9 in 2018, losing its last three games by an aggregate score of 100-41.
This is the Dolphins' first full-time, defensive-minded head coach hire since Nick Saban in 2005. Flores, a linebacker coach whose role got elevated to playcaller when Matt Patricia left to take the Detroit Lions head coach job in 2018, will have some young core defensive players to build around, like budding star cornerback Xavien Howard, versatile defensive back Minkah Fitzpatrick and promising playmaking linebacker Jerome Baker. Safety Reshad Jones and Kiko Alonso are also strong established veterans to help the transition.
The Dolphins allowed 6,257 yards this past season, 29th in the NFL and the most in franchise history. The offense, which finished 31st, wasn't any better.
Ross reiterated that the Dolphins are taking a "different direction," and it may take multiple years for Miami to be ready to compete for a championship.
The Dolphins also interviewed Cowboys defensive playcaller Kris Richard, Chiefs offensive coordinator Eric Bieniemy, Saints defensive coordinator Dennis Allen and their own special teams coordinator, Darren Rizzi, for the head job. Ultimately, they decided Flores was the right man.
Flores is coming off maybe his best performance as a coach. He helped devise a scheme and called the plays for a Patriots defense that held Sean McVay's Rams to just three points in Super Bowl LIII, tied for fewest in Super Bowl history, and 260 total yards. To use McVay's own words, he was "outcoached" by Flores, Belichick and the Patriots defense.
After the Patriots' win Sunday, Belichick credited Flores with making the blitz call that ended in a Jared Goff interception late in the fourth quarter. Goff said the Patriots defense had them "completely guessing."
Less than 24 hours later, Flores is now running his own show as Miami's coach.
"It has been a whirlwind 24 hours," Flores said with a smile at a news conference that drew two dozen cameras.
Among those attending the news conference were Flores' wife, Jennifer, their three children and his high school coach. Also on hand was the last quarterback to lead Miami to a Super Bowl, Dan Marino, in 1984, and the last quarterback to help the Dolphins win one, Bob Griese, in 1973.
The Associated Press contributed to this report.