Cooks played at Oregon State from 2011 to 2013. As a true freshman in 2011, he played in all 12 games with three starts. He finished the season with 31 receptions for 391 yards and three touchdowns. He was also a kick returner averaging 22.4 yards a return. As a sophomore in 2012, he had 67 receptions for 1,151 yards and five touchdowns. The combination of Cooks and Markus Wheaton created one of the most dynamic receiving duos in college football and Oregon State history. The two players combined for 158 receptions, 2,395 yards and 16 touchdowns.
During his junior year in 2013, he had 128 receptions, 1,730 receiving yards and 16 touchdowns. The receptions and receiving yards were Pac-12 records. He was held to under 100 yards only four times and exceeded 200 yards in a game twice. At the end of the season he won the Fred Biletnikoff Award and was a consensus All-American. He was the second Oregon State player to win the Biletnikoff Award, the first being Mike Hass in 2005.
On January 2, 2014, Cooks announced that he would forgo his senior season and enter the 2014 NFL Draft.
Cooks also ran track at Oregon State. He earned a second-place finish in the 60-meter dash at the 2012 UW Invitational, clocking a personal-best time of 6.81 seconds.
Cooks was selected by the New Orleans Saints as the 20th pick of the first round of the 2014 NFL Draft; the Saints traded up from the 27th spot, giving their first and third round picks to the Arizona Cardinals in return for Arizona's first round pick, in order to get Cooks. On May 18, 2014, the Saints signed Cooks to a four-year contract worth $8.3 million.
In his first career game, Cooks caught seven passes for 77 yards and a touchdown in a narrow loss to the Atlanta Falcons. Cooks had 53 catches for 550 yards and 3 touchdowns before breaking his thumb in Week 11, ending his season.