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.
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.
In February 2010, Fowler finished second at the Waste Management Phoenix Open with a score of 15-under-par at the TPC of Scottsdale course. In June, Fowler notched his third PGA Tour runner-up finish at the Memorial Tournament in Dublin, Ohio. Fowler entered the final round in the lead, but shot a 73 to finish behind Justin Rose, who recorded his first PGA Tour victory. This performance took Fowler into the top 50 of the Official World Golf Ranking.
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.