Lowry started his youth career with Australian club ECU Joondalup. He signed for Aston Villa in February 2005 along with fellow Australian Chris Herd. Lowry made nine appearances for Aston Villa Reserves in the 2006–07 season, mainly coming near the end of the campaign. Lowry was also part of the squad that won the HKFC International Soccer Sevens in May 2007. In June 2007, Lowry signed a 12-month deal to his contract.
At the first FedEx Cup playoff event of the season, The Barclays, Fowler went into the final round leading the event by one stroke. He endured a difficult final round, shooting a two-over-par 74. His challenge was ended with a double-bogey at the 16th hole that put him four strokes behind playing partner Patrick Reed. He went on to finish T7, three strokes behind the winner Reed. As a result of this, Fowler also failed to secure his automatic Ryder Cup spot, which he would have done with a top-three finish. Fowler moved up from 28th to 16th in the FedEx Cup standings with this result.
At the 2016 U.S. Open at Oakmont Country Club near Pittsburgh, Lowry shot 65 (−5) in the third round for 203 (−7) and a four-stroke advantage over Dustin Johnson and Andrew Landry at the 54-hole stage. The 65 was Lowry's joint career best round at a major championship. Due to weather delays on Thursday, the third round was not completed until early on Sunday, and Lowry birdied two of his remaining four holes to extend his two stroke overnight lead to four. In the final round he was in contention for the title, within one shot of Dustin Johnson after 12 holes, before three consecutive bogeys on holes 14, 15 and 16 ended his chances. He finished the tournament tied for second place, with a final round score of 76.
On 23 November 2011, Lowry was again loaned out to play in the Championship, this time to Millwall until 3 January 2012. He followed Aston Villa team-mate Nathan Baker who also signed on loan for Millwall two days earlier. Lowry made his Millwall debut three days later, where he played 90 minutes, in a 0–0 draw against Crystal Palace. His impressive display at Millwall soon earned a loan extension. Weeks later on 13 January 2012, Lowry was sent-off in the 22nd minutes after stamping on Nikola Žigić, which saw Millwall lose 6–0. Three years on after signing for Birmingham City, Lowry stated, quoting: "Whatever club I play for I fully commit to that club at the time. I play with my heart on my sleeve. Sometimes in the past I have gone overboard but I was a younger player then, I have learned a lot from these types of experiences. But I am an aggressive player, that’s the way I like to play and I can’t change the way I play. I will use my experience now and be a bit more clever."'
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.
In 2008, Fowler repeated as Sunnehanna Amateur champion. In the first round of the U.S. Open, Fowler shot a −1 (70) and was in a tie for 7th place. He was one of three amateurs to make the cut, along with Derek Fathauer and Michael Thompson. He ended the tournament tied for 60th. In October 2008 Fowler played on the Eisenhower Trophy team that finished second. He was the leading individual player.
Lowry elected to turn professional the week after his Irish Open triumph, meaning that he would miss out on the opportunity to play in the Walker Cup in September 2009. He made his professional début on 28 May at the European Open, where he shot 78 in the first round to end the opening day almost at the back of the field, and went on to miss the cut following a second round 73.