He was the youngest player ever to represent Australia in the Eisenhower Trophy and he won the Holden Australian Open as an amateur in 1999 and retained his title in 2000, by which time he had turned professional.

He had second-place finishes on the PGA Tour in 2003 at the Sony Open in Hawaii and 2004 at the Chrysler Classic of Tucson.

However he struggled for consistency, and after a solid rookie season, when he finished 73rd on the money list, he only just retained his card in 2004, when he came 124th.

Baddeley was the leader after the third round of the U.S. Open at Oakmont Country Club on 16 June 2007 with a two over par score of 212 (72-70-70).

After a lull in form over the following few seasons, where he was finishing only in the lower reaches of the top-125 on the money list, Baddeley returned to the winner's circle when he won the 2011 Northern Trust Open in California.

In October 2011, Baddeley was selected by Greg Norman as one of his two wildcard picks for the 2011 Presidents Cup team.

He earned his first win in five years at the 2016 Barbasol Championship, beating Kim Si-woo in a four-hole playoff.

Baddeley is a committed Christian and has confessed that it was his faith that prevented him giving up professional golf on numerous occasions.