In 2006, Fowler shot a 137 for two rounds at the U.S. Junior Amateur and was knocked out in the second round of match play. The championship was won by Philip Francis.

Fowler represented the United States in their victory at the 2007 Walker Cup. His record was 2-0 in foursomes and 1-1 in singles making his overall record 3-1. Billy Horschel was his partner for both of their foursome victories. In the summer of 2006 Fowler won the Western Junior and competed in the U.S. Amateur and was defeated by the eventual champion Richie Ramsay.

In 2007, Fowler won the Sunnehanna Amateur in June and the Players Amateur in July.

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, he played on the Eisenhower Trophy team that finished second.

In 2009, Fowler made his second and last appearance in the Walker Cup. He won all four matches he played in as the U.S. won by a seven point margin.

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 threeway playoff that included Jamie Lovemark. Fowler's impressive 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.