Lowry missed the first three cuts of his professional career, but had his first payday on 5 July, when he finished 50th at the Open de France ALSTOM. He had his best professional result in November 2009, when he finished 3rd in the Dunlop Phoenix Tournament in Japan. In January 2010, Lowry finished in fourth place in the Abu Dhabi Golf Championship, moving him into the top-100 of the Official World Golf Ranking.
Deutsche Bank Championship: Shot a final-round 3-under 68 to come from one shot back and defeat third-round leader Henrik Stenson at the Deutsche Bank Championship, good for his third career PGA TOUR victory. Earned the win at age 26 years, 8 months, 25 days in his 150th career start. Collected 2,000 points and moved from No. 22 to No. 3 in the FedExCup standings. Has come from behind to win all three of his PGA TOUR events, with his first two wins via playoffs (2012 Wells Fargo Championship and 2015 PLAYERS Championship). Became the sixth consecutive come-from-behind winner at TPC Boston.
Lowry started for Leeds in the Football League Trophy Northern Area Final, second leg game against Carlisle United, in which the game was lost with Lowry missing the decisive penalty in sudden death in the penalty shootout. After the game it appeared as though Lowry was attacked by a set of Carlisle supporters who had invaded the pitch. After starting every game for Leeds Lowry was dropped from the Leeds squad for the match against Brentford after suffering an injury, before returning to Villa when his loan spell ended. On 25 March 2010 Lowry re-signed for Leeds for a second loan spell, with his loan lasting until the end of the season. Lowry started at left back for Leeds against Norwich City on his return to the club, a match Leeds went on to lose 1–0 in injury time. Lowry didn't overley impress the Leeds fans in his loan spell at Leeds, with him being mostly played out of position at Left back for the entire spell, he was substituted for Jonathan Howson in the final game of the season against Bristol Rovers with 1–0 down at the time, but his loan spell ended on a high as Leeds were promoted in 2nd place after scoring two goals to go on and beat Bristol Rovers and secure promotion to The Championship.
Nationwide Tour Players Cup: Playoff runner-up to Derek Lamely at the Nationwide Children's Hospital Invitational. Started the final round five shots behind 54-hole leader Dave Schultz. Held the lead during much of the final round but suffered a bogey at the 72nd hole of regulation to drop into a tie with Lamely and force a playoff. Lost to Lamely when he failed to get up and down from a greenside bunker on the second extra hole, missing his par putt of 12 feet. Lamely rolled in a three-foot par putt to win.
Hyundai Tournament of Champions: Finished T6 in a Monday-start-Tuesday-finish event, the season-opening, 54-hole Hyundai Tournament of Champions. The event "started" twice during the regularly scheduled first round Friday and later Sunday, but both times PGA TOUR rules staff halted play due to unplayable windy conditions and subsequently voided all scores that had taken place. As the first player off the tee, he ended up hitting three "opening" shots of the season.