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."'
The Open Championship: Enjoyed his best finish among seven major championship starts, with a T5 at The Open Championship at Royal St. George's. Opened with three par-or-better rounds to enter the final round three strokes behind Darren Clarke. Closed with a 2-over 72 in windy conditions to finish tied with fellow Americans Chad Campbell and Anthony Kim.
In May 2012, Fowler won the Wells Fargo Championship in Charlotte on the first extra hole of a sudden-death playoff. Replaying the 18th hole, he defeated Rory McIlroy and D. A. Points with a birdie to gain his first PGA Tour win. Fowler shot a 69 (−3) in the final round to finish in a three-way tie after 72 holes at Quail Hollow Club. This win enabled Fowler to break the top-25 in the world, placing him at number 24. The following week at The Players Championship in Ponte Vedra Beach, Florida, Fowler played the final hole at −11 under par and had a birdie opportunity to bring him within one of leader and eventual winner Matt Kuchar. Fowler, however, pushed his putt to the right and finished in a tie for second, the fifth second-place finish of his career.
Lowry made his debut for the Glory on 30 January 2016, starting against Melbourne Victory. Lowry then scored his first Perth Glory goal on 20 February 2016 when he scored a header in the 41st minutes, to give Brisbane Roar a thrashing with a 6–3 win for Perth Glory. Throughout the 2015–16 season, Lowry established himself in the starting eleven and formed a central defense partnership with Alex Grant, as he made ten appearance for Perth Glory in his first half of the season.
While serving a suspension, Lowry signed a two-and-a-half-year permanent deal to Millwall for an undisclosed fee on 27 January 2012. Lowry then made his first appearance for the club since joining Millwall permanently, playing 90 minutes, in a 2–1 loss against rivals' West Ham United on 4 February 2012. Right way through March, Lowry was sidelined with ankle injury that kept him out for weeks. After making his first team return against Cardiff City, in a 0–0 draw on 31 March 2012, Lowry scored his first Millwall goal, which he scored the only goal in the game, in a 1–0 win over Coventry City on 17 March 2012. Lowry finished his 2011–12 season, making twenty-two appearance and scoring once.
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.
U.S. Open: Established the first-round lead at the U.S. Open with a 7-under 65 and was in the mix all week at Erin Hills. Followed with 73 to be one back through 36 holes. Third-round 68 had him two adrift headed into final round. Closed with even-par 72 to finish six back of Brooks Koepka at T5. In nine U.S. Open appearances, has advanced to the weekend five times and never broken par in the final round.
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.