She played the Korean Tour again in 2003 and moved on to the LPGA Futures Tour the following year, winning her ticket to the full Tour for the 2005 season. Having won the Canadian Open, she was second to Paula Creamer as Rookie of the Year 2005.

In 2006, Lee won her second LPGA event after a three-hole, sudden-death playoff with Seon Hwa Lee at the Fields Open in Hawaii, where she crossed the $1 million mark in career earnings and carded a career-low 65 during the final round; also carded a 65 in the opening round of the LPGA Corning Classic, but lost to Hee-Won Han in a four-hole, sudden-death playoff.

In 2007, the Korean recorded a season-best tie for eighth at both the Ginn OPEN and the Hana Bank  KOLON Championship 2007.

In 2008, Lee recorded a season-best runner-up finish at the P&G Beauty NW Arkansas Championship Presented by John Q. Hammons, where she tied her career-low 65 in the second round; also carded a 65 in the second round of the Wegmans LPGA, where she finished tied for 16th; crossed the $2 million mark in career earnings at the U.S. Women's Open; led the LPGA Tour in driving accuracy, hitting 79.8 percent of fairways.

In 2009, Lee recorded a season-best tied for third at the Evian Masters Presented by Societe Generale, where she tied a career-low 65 in the final round.

In 2011 Lee finished T-6 at the Wegmans LPGA Championship and improved on that in 2012 by finishing T-2 at the LPGA LOTTE Championship. Another top 10 finish was added during 2012 in a year which saw her make 22 cuts.