He played college football for the LSU Tigers and was selected by the Green Bay Packers in the seventh round of the 2008 NFL draft.

He also played for the Seattle Seahawks, Oakland Raiders, Buffalo Bills, New England Patriots, New York Jets, and New Orleans Saints.

[1] Matthew Flynn attended Robert E. Lee High School where he was coached by Mike Owens, and was teammates with Justin Warren, Brandon Pettigrew, and Ciron Black.

[5] As a junior in 2001, Matthew Flynn completed 101 of 199 passes for 1,650 yards, 13 touchdowns and 9 interceptions for the season, leading Lee to the 5A-I playoffs, where they lost in the second round to eventual state champion Mesquite High School.

Matthew Flynn displayed toughness by leading Robert E. Lee High School to a semifinal appearance despite playing his last four games with a broken foot.

[7] After his senior season, 247 Sports listed Matthew Flynn as the top-rated Texas high school quarterback in 2003.

Flynn also made a short appearance in the 2004 Capital One Bowl, completing 1 of 4 passes for 11 yards in a 25–30 losing effort against Iowa.

The departure of Randall left Russell and Flynn battling for the starting quarterback position in the 2005 season.

In a win over North Texas, Flynn threw a perfect 7-of-7 for 139 yards and 3 touchdowns, all in the fourth quarter.

Flynn and the Tigers then beat Louisiana Tech the following weekend and climb back to the #1 spot after a loss by then-#1 Ohio State.

On January 7, 2008, Flynn led LSU to a BCS National Championship, beating Ohio State 38–24.

[18][19] In 2008, Flynn won the competition for the back-up role to Aaron Rodgers, beating out fellow rookie and second-round pick Brian Brohm.

[28][29][30] He was brought in to compete with 2013 NFL draft fourth round pick Tyler Wilson and 2011 NFL draft supplemental third round pick Terrelle Pryor for the starting quarterback position,[31] with Pryor winning the starting job in preseason.

Flynn relieved an injured Pryor in a Week 3 match-up against the Broncos, completing 1 of 2 passes for 19 yards in a 37–21 loss.

Several days later, Raiders coach Dennis Allen announced Flynn's demotion to third-string behind Pryor and undrafted rookie Matt McGloin.

[33] On October 14, 2013, Flynn worked out with the Buffalo Bills with rookie and starting quarterback EJ Manuel out 6–8 weeks with a knee injury, and backup Thad Lewis injured during a game against the Cincinnati Bengals.

Flynn did not see any playing time in Buffalo and primarily served as an emergency replacement should third-string quarterback Jeff Tuel also be hurt.

Flynn would add a veteran presence for second-year quarterback Jimmy Garoppolo for four games due to the suspension of Tom Brady.

On September 3, 2015, Flynn started the Jets' preseason week 4 match-up against the Philadelphia Eagles, throwing 10–14 for 136 yards, 2 touchdowns, and 1 interception.

On November 15, 2015, Flynn was signed by the New Orleans Saints after back-up quarterback Luke McCown suffered a season-ending injury.