In 2004, he led Nova Seafood to the American Legion World Series Championship, as well as winning the Telegram League batting title.

[2] 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.

[3][4] As a sophomore, Flaherty had a .381 batting average with 57 RBI, 23 doubles, four homers and an on-base percentage of .438 in 67 games.

[7] 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.

On September 28, 2012, he hit his first career grand slam off Boston Red Sox pitcher Aaron Cook.

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.

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.

[16] On September 2, the Braves select Flaherty's contract, adding him back to the major league roster.

[17] He was active on the Braves NLDS roster as a bench player alongside Lane Adams, Lucas Duda and René Rivera.

After being informed he would not make the opening day major league roster, Flaherty opted out of his contract on March 20, 2019.

[19] Flaherty re-signed on a minor-league deal on March 31 and the organization assigned him to their Triple–A affiliate, the Columbus Clippers.