He is the son of Edward and Deborah Flaherty. Edward was a star at the University of Maine and is now the head coach at the University of Southern Maine, a division III school in Gorham, Maine. He has been there for 32 years and the field at USM is named for him. As a kid, Ryan would accompany his father to Southern Maine practices, and field grounders. His younger brother, Regan was a draft pick of the Seattle Mariners. Flaherty graduated from Deering High School in 2005. In 2004, he led Nova Seafood to the American Legion World Series Championship, as well as winning the Telegram League batting title. He was a 2005 American Baseball Coaches Association Preseason All-American, also winning Maine’s Mr. Baseball award in honor of John Winkin. He was also named Maine Gatorade High School Player of the Year as a senior at Deering High School. Flaherty lettered in baseball, basketball, captained the football team and was a finalist for the Fitzpatrick Trophy, which is given to Maine’s best football player.

As a freshman, Flaherty was named an honorable mention Freshman All-American. In sixty-two games, Flaherty had a .339 batting average with 49 RBI, 19 doubles, two homers and an on-base percentage of .421, leading the team with 22 multi-hit and 15 multi-RBI games. In 2006, he played collegiate summer baseball with the Hyannis Mets of the Cape Cod Baseball League.

The Chicago Cubs selected Flaherty in the first round (41st overall) of the 2008 MLB draft. In four seasons in both A and AA, Flaherty played 322 games with a .279 batting average, on-base percentage of .347, slugging percentage of .455, 182 RBI, 38 homers and 79 doubles. He had his two best professional seasons in 2009 and 2010. While in the Cubs organization he was ranked as the 8th best prospect.

The Baltimore Orioles selected Flaherty from the Cubs in the Rule 5 Draft on December 8, 2011. He made the Orioles’ Opening Day roster. He scored his first run in the MLB on April 14 against the Blue Jays in Toronto. He had his first MLB RBI on April 26, 2012, when he drove in Chris Davis on a sacrifice fly in the bottom of the fifth inning off of Drew Hutchinson of the Toronto Blue Jays. In that same game, he collected his first MLB hit on a bunt single in the bottom of the seventh inning off of Luis Perez. He hit his first MLB home run as part of three consecutive home runs off Colby Lewis of the Texas Rangers to start the first inning of the first game of a May 10, 2012, doubleheader at Camden Yards. Teammates J. J. Hardy and Nick Markakis followed with home runs.

Flaherty bats left-handed and is considered to have good batting power for an infielder. On September 28, 2012, he hit his first career grand slam off Boston Red Sox pitcher Aaron Cook. On October 10, 2012, Flaherty hit a home run in Game 3 of the 2012 American League Division Series, becoming the first native of Maine to hit a home run in the MLB postseason. Flaherty had his first multi-home run game on June 23, 2013 against the Toronto Blue Jays.

Ranked the 141st-best professional prospect by Baseball America, he chose to attend Vanderbilt University, where he played college baseball for the Commodores in the Southeastern Conference (SEC) of the National Collegiate Athletic Association’s Division I alongside fellow future Major League players David Price and Pedro Alvarez; the latter became a teammate on the Baltimore Orioles in 2016.

Flaherty became the seventh position player to make a pitching appearance in Orioles history in a 12–2 loss to the Houston Astros at Camden Yards on August 20, 2016. He had entered the game as a third baseman in the eighth inning. Throwing 19 pitches in the ninth, he surrendered two earned runs and three hits on a leadoff homer by Jason Castro and consecutive one-out doubles from George Springer and Alex Bregman.

Flaherty married Ashley Dutko, the sister of Nick Markakis’ wife Christina Dutko, in 2016.

On February 9, 2018, Flaherty signed a minor league deal with the Philadelphia Phillies. He was released on March 22.

On March 26, 2018, the Atlanta Braves signed Flaherty to a one year contract worth $750,000. He was designated for assignment on August 20, and outrighted on August 23. He was active on the Braves NLDS roster and appeared in games 3 and 4

On February 7, 2019, Flaherty signed a minor league deal with the Cleveland Indians. After being informed he would not make the opening day major league roster, Flaherty opted out of his contract on March 20, 2019. Flaherty re-signed on a minor-league deal on March 31 and the organization assigned him to their AAA affiliate, the Columbus Clippers. On September 1, the Indians selected Flaherty’s contract.

Following the 2019 season, on November 24, Flaherty became an advance scout and development coach for the San Diego Padres.