Thompson began his college career at Washington State University in Pullman, Washington. He played for the Cougars for three seasons, from 2008-2011, and made an immediate impact as a freshman. In his first year, Thompson started all 33 games, leading his team in 3-point field goal percentage and free throw percentage, and averaging 12.5 points per game. He was named to the Pac-10 All-Freshman Team and Collegehoops.net All-Freshman Honorable Mention Team.

As a sophomore, Thompson continued to improve and set new records. He led the Cougars to the Great Alaska Shootout Championship, being named its Most Outstanding Player after scoring a tournament single game record of 43 points in its championship game. This was also the third-highest single-game point total in WSU history. After becoming the third fastest Cougar to reach 1,000 points, Thompson was named to the All-Pac-10 First Team. He earned Pac-10 Player of the Week honors twice during the season and was chosen as a midseason candidate for the John R. Wooden Award. Thompson finished the season averaging 19.6 points, good for second in the conference.

Thompson's junior year was arguably his best at Washington State. He led the Pac-10 in scoring, again earning All-Pac-10 first team honors. He became just the third Cougar to win first-team all-district honors from the National Association of Basketball Coaches twice in his career. In addition, he became the first Cougar to be named Pac-10 Player of the Week three times when he won the award for the week of Nov. 22-28, extending the record to four after the week of December 6-12. Soon after, Thompson was named one of the 30 midseason candidates for the John R. Wooden Award. In the 2011 Pac-10 tournament, he set tournament records with 43 points and eight three-pointers. Thompson finished the season by setting WSU's single-season scoring record with 733 points, making him the third all-time leading scorer in WSU history.

Overall, Klay Thompson had an outstanding college career, earning numerous awards and accolades along the way. His success on the court helped prepare him for the rigors of the NBA and set him on a path to greatness. As a Golden State Warrior, Thompson has continued to excel, demonstrating the skills and dedication that made him one of the top players in the country during his college days at Washington State.