In July 2009, he helped lead them to the semifinals in the Star Vision Sports Center Stage tournament in Las Vegas.

Despite the hype around the Baylor basketball program coming into the season, the Bears finished with a record of 18–13 (7–9 Big 12) and failed to make the NCAA Tournament.

Despite Baylor's struggles Perry Jones was still named to the All-Big 12 Second Team along with Kansas junior Markieff Morris, Texas freshman Tristan Thompson, Iowa State senior Diante Garrett, and Texas A&M sophomore Khris Middleton.

[7] On March 10, 2011, NCAA investigators ruled Perry Jones ineligible for receiving improper benefits from his AAU coach prior to enrolling at Baylor University (The benefits were reportedly three 15-day loans to Jones' parents totaling less than $1,000, all of which were paid back).

[9] Jones was a projected lottery pick in the 2012 NBA draft, but fell to 28th overall when he was selected by the Oklahoma City Thunder.

[12] On October 30, 2014, Jones scored a career-high 32 points on 10-of-17 shooting in the 90–93 loss to the Los Angeles Clippers.

[24][25] On January 2, 2022, Jones cleared waivers and was acquired by the Windy City Bulls via the available player pool.

[30] On May 26, 2024, Jones signed with the Spartans Distrito Capital of the Superliga Profesional de Baloncesto (SPB).