As a 14-year-old in 2009, she qualified for a third time for the U.S. Women's Open and made the cut for the first time, finishing tied for 34th on +11.

Thompson announced that she had turned pro on June 16, 2010 and after three professional events, her earnings were $314,842, which would have ranked 18th on the official LPGA money list if she had been a member of the LPGA Tour.

In September 2011, she won her first LPGA tournament, the Navistar LPGA Classic by a five-stroke margin over LPGA Tour rookie Tiffany Joh. At age sixteen she became the youngest winner ever on the LPGA Tour, breaking the previous record set by Marlene Hagge at age 18 in 1952. On December 17, 2011, Thompson won the Dubai Ladies Masters, an event on the Ladies European Tour (LET), with a four stroke margin. This win made her the youngest professional winner on the LET at age 16 years, 10 months, 7 days.

Thompson successfully petitioned the LPGA to receive a waiver to the rule that LPGA Tour members must be at least 18 years old, allowing her to enter the 2011 LPGA Qualifying School for Tour membership in 2012. The first of three stages was held July 26–29 at the LPGA International course in Daytona Beach, Florida. Thompson won Stage I by 10 strokes, shooting -23 (66-66-66-67=265). The top 50 finishers and ties from the first stage advanced to Stage II. After winning the Navistar LPGA Classic, Thompson withdrew from qualifying school and petitioned the LPGA for membership based on her win.

Thompson’s highlight of 2012 was undoubtedly her season-best finish as runner-up at the Navistar LPGA Classic where she recorded a career low 63 in the first round. She went on to record 4 top 10 finishes and make 19 cuts.