"It's a dream of a lifetime," said Flynn, 45, who will live in Pensacola, Fla., with his wife; two sons, 8 and 10; and a daughter, 6. "There is only one Blue Angel team."
He will help oversee 130 men and women - officers and enlisted sailors and Marines - as they put on as many as 70 air shows a year to showcase the "pride and professionalism" of the services through flight demonstrations and community outreach.
"We want to inspire people to consider the Navy and Marine Corps as a career," said Flynn. "That's what we exist for.
"We want to recruit the best possible young men and women. We have top-notch people and we want to keep that going."
Flynn said he will support the flight leader of the Blue Angels - Cmdr. Tom Frosch - "in the day-to-day operations of the squadron. I won't be flying, but I'll make sure that we have the people and the parts - everything needed to do the mission."
Flynn attended Moorestown High School and played football with a fellow student whose father graduated from the U.S. Military Academy at West Point and took the two to Army-Navy games in Philadelphia.
The exposure to the military prompted him to investigate the possibility of attending one of the academies. "I chose the Navy because it offered so many diverse careers," he said. "You could fly jets, sail ships, and serve on submarines."
During the 1990s, Flynn flew missions in Operation Decisive Endeavor, providing security in Bosnia, and in Operation Southern Watch in southern Iraq, helping contain Saddam Hussein and encouraging him to cooperate with weapons inspectors. He also flew missions off the carrier Harry Truman during Operation Iraqi Freedom in 2004.
In 2009, Flynn helped supervise efforts around Basra to stop the IEDs that were wounding and killing so many Americans and allied soldiers running convoys through southern Iraq.
"We would run jammers to jam the device, and made sure the pre-convoy checks were done and that we adhere to all the things we needed to do," he said.
Flynn became a military professor at the Naval War College about four years ago, and said he came to New Jersey to see family frequently.
"Moorestown is still my home of origin," he said. "It's a place I go regularly, where I still have high school friends.
"It was a great place to grow up and go to school. My mom is there; I have two brothers living in Delran, and another one who is the principal of Burlington City High School and lives in Downingtown."
Many Navy and Marine Corps officers submit applications to join the Blue Angels each year, the Navy said.
"We remain committed to selecting the most talented and qualified individuals to join the Blue Angels," said Frosch, the team's commanding officer. "We are proud of those we have chosen to join the 2015 team. They are excellent representatives of the skilled service members defending our freedom around the world."
The Blue Angels select finalists to interview at the home base at Naval Air Station Pensacola during the week of the Pensacola Beach Air Show in July. The team makes selections at the conclusion of the interview week.
The Blue Angels "practice six days a week - 120 times between November and March - before they do a single show before the public," said Flynn. "I'm proud to be with such an amazing group of people."