Lindsay began her basketball career at the Hutchinson High School in Minnesota. She had a flawless record of having a four-time respectable Minnesota Conference preference. She compelled her team to three separate, successive Basketball Conference Championships. She went on to win a state title as well as 13th place in combination with the Minnesota Jaguars, her club team. If that alone is not impressive enough, she was also an All-Conference preference pick in both track and tennis as well. Throughout her high school career in basketball, she rounded out at 5.8 rebounds, 22.8 points, as well as 4.3 assists for her stats at the end of her junior year. A finalist for the wade trophy, She graduated as a senior and went on to play at the University of Minnesota women's basketball program.  

During Lindsay Whalen's career at the University of Minnesota women's basketball program, she escorted the team to national recognition and prominence. Attendance on average at the women's basketball games more then quadrupled from 1,087 at the start of her freshman year, to an impressive 9,866 at the start of her senior year. Eventually, rising up to Minnesota's all time top scorer, Lindsay Whalen surpassed the 1994 Carol Ann Shudlicks Wade Trophy win. This impressive benchmark was reached at the game against Michigan State on the date of January 25, 2004. Lindsay Whalen's college career was concluded with a total of 2,285 points. The number 5 best in the history of the Big Ten Conference.

Lindsay Whalen has several Minnesota records in scoring average, free throws made, free throw percentage, points, and games in double figures. She also boasts a place among the top ten in field goal percentage, field goals made, three pointers made, three point field goal percentage, field goal attempts, free throws attempted, assists, three pointers attempted, and steals. Lindsay was a Wade Trophy Finalist twice consecutively, in 2003 and 2004. The first Golden Gopher to gain All-American honors, Lindsay Whalen earned this in three separate seasons. Due to her tremendous accomplishments at the University of Minnesota, her jersey number of 13 was officially retired in a ceremony at Williams Arena in January of 2005.

The first round of the 2004 draft for WMBA, (4th overall) Lindsay Whalen was drafted by the Connecticut Sun. In the Big Ten Conference, Whalen was the highest drafted WMBA player ever until Janel McCarville, a fellow teammate, was chosen as number one in 2005. During a failed pre draft trade, the Minnesota Lynx sent Sheri Sam along with Janell Burse off to the Seattle Storm in exchange for the 6th pick in the draft and Amanda Lassiter in a bid to get Lindsay Whalen. Unfortunately, before Minnesota got the chance, Connecticut chose Whalen. 

Lindsay Whalen was picked in her rookie season to play at Radio City Music Hall in the historic USA Basketball vs.. WNBA. Lindsay was injured in 2005, but none the less continued to play, and she led the Connecticut Suns to the WMBA Finals during her first and second seasons. While a noble accomplishment in itself just to get there, unfortunately, Whalen and the Connecticut Suns were defeated by the Seattle Storm and Sacramento Monarchs both years in the Finals.