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.
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.
THE PLAYERS Championship: After beginning the final round of THE PLAYERS Championship three strokes off the lead, at 7-under 209, played his last six holes in 6-under to post a 6-under 66 and join a three-hole aggregate playoff with 2008 PLAYERS champion Sergio Garcia and Kevin Kisner. Finished birdie-par-birdie-eagle-birdie-birdie on Nos. 13-18 in regulation. Played Nos. 15-18 in a 5-under total of 11 strokes. The four-hole score of 11 set a new single-round low for the final four holes at TPC Sawgrass. Previously, seven players had finished with a score of 12 on the final four holes. When Garcia was eliminated after the aggregate playoff, Fowler and Kisner returned to the famed, par-3 17th for sudden death. Fowler converted a 4-foot, 8-inch putt for birdie to claim the title. Before his back-nine charge, his mother had made her way to the airport to leave town. A text message alerting her to her son's rally resulted in her immediate return to TPC Sawgrass in time to witness the win. With the victory, moved to ninth in the Official World Golf Ranking and No. 7 in The Presidents Cup standings.
Fowler's first PGA Tour event as a professional was the Justin Timberlake Shriners Hospitals for Children Open where he finished tied for seventh. His second PGA Tour event was at the Frys.com Open played at Grayhawk Golf Club in Scottsdale, Arizona. He finished tied for second after losing to Troy Matteson in a three-way playoff that included Jamie Lovemark. Fowler's score of 18-under-par included a hole-in-one on the fifth hole in his final round. Fowler also notched an eagle in each of his four rounds.
With this win, he entered the Official World Golf Ranking as an amateur at No. 168 and reached a career high of sixth in the World Amateur Golf Ranking. Walker Cup captain Colin Dagleish described the win as "fairytale stuff", adding: "You'd have to say that Shane's victory was the biggest (of the three amateur wins). To win your own national Open is quite something. It was unbelievable, it really was." The win was only the second home victory since 1982 and the first since Pádraig Harrington in 2007. Harrington himself was also full of praise: "It's fabulous for Irish golf. You only have to look at the fact it is such a rarity for an amateur to win, such a rarity for an Irish player to win the Irish Open. So, on a lot of fronts, it is a big deal. It was very impressive."
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.
In September, he signed a clothing deal with Puma. In the same month, he was also chosen as a captain's pick for the U.S. Ryder Cup team. At age 21 years and 9 months when the matches began, Fowler became the youngest U.S. Ryder Cup player of all time, and only European Sergio García was younger when he made his Ryder Cup debut in 1999. Fowler forfeited a hole during foursomes competition on the first match day because of a rules violation, by taking a permissible free drop from muddy conditions in an improper location, a mistake U.S. captain Corey Pavin attributed to Fowler's inexperience. On the final day of the competition in his singles match against Edoardo Molinari, Fowler birdied the last 4 holes to halve the match after having been 4 down after 12 holes.
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.
At the PGA Championship, Fowler carded 74-69-75-68 to finish with a six-over par total of 286, in a tie for 51st place. Early on the third day Fowler rocketed up the leaderboard with three birdies in the first five holes only to falter later in the round with two triple bogeys, effectively ending his hopes of a first major championship and PGA Tour win.
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.
In June 2015, he became the first SMU Mustang to win the NCAA individual championship, recording a score of 280 (−8) to win by one stroke. In August, he won the U.S. Amateur title, defeating Derek Bard 7 & 6 in the 36-hole final. He became the fifth player to win both the NCAA and U.S. Amateur titles in the same year, joining Jack Nicklaus (1961), Phil Mickelson (1990), Tiger Woods (1996), and Ryan Moore (2004).
The form and fitness of centre-backs Michael Morrison and Jonathan Spector and left-back Jonathan Grounds restricted Lowry to a seat on the bench until mid-December. He eventually made his debut in the starting eleven for the home fixture against Cardiff City on 18 December, standing in for the injured Grounds at left back. He appeared once more, in the FA Cup, before his contract was cancelled by mutual consent to enable him to return to Australia.
Frys.com Open: At the Frys.com Open in Scottsdale, Ariz., reached a three-way playoff with Jamie Lovemark and eventual-winner Troy Matteson. Began the final round four strokes behind Matteson, but played his first five holes in 5-under, punctuated by a hole-in-one from 211 yards at the par-3 fifth hole. After finishing T2 in the playoff, he had recorded all eight of his professional rounds in the 60s. Thanks to the T7 in Las Vegas at the Justin Timberlake Shriners Hospitals for Children Open and T2 finish at Grayhawk GC, he surpassed No. 150 from the 2008 money list, earning special temporary membership on TOUR for the remainder of the season.