Cortines served as LA's interim superintendent for several months in 2000, before former Colorado governor Roy Romer assumed the position.

[9] The Los Angeles Times reported that he was paid $150,000 while serving at the Scholastic board, in addition to $250,000 as Superintendent of LAUSD.

Cortines defended his tenure at Scholastic, and claimed he avoided any issue which involved the educational publishing company.

A notable controversy occurred six months after Cortines was named Superintendent of LAUSD, after he proposed to reduce funding for the Office of Inspector General (OIG) by 75%.

[11] Thornton had previously produced audit and investigative reports that showed misuse of funds, lack of financial controls and many conflict-of-interest charges against senior district management.

A notable report was released four months after Jerry Thornton's departure, which found “irregularities in $65 million worth of consultant contracts.”[14] This includes costs that exceeded pre-approved amounts by 50% and additional contracts worth $31 million without school board approval, specifically against James Sohn, Chief of Facilities, whom Cortines had hired to replace the prior chief, Guy Mehula.

[15] Cortines originally retired as superintendent of the Los Angeles Unified School District on April 16, 2011.

[17][18] On December 15, 2015, Cortines ordered all LAUSD schools to close for the day after receiving a bomb threat.