Last Tuesday, Thompson sent a memo to Yahoo employees, apologizing for the distractions that the company is dealing with. He did not, however, make any reference to his resume.

That same day, Yahoo announced that director Patti Hart would not seek re-election to the board at the company's 2012 annual shareholder meeting. Hart led the search committee that hired Thompson, and was criticized for not fully vetting Thompson's resume.

Yahoo's board of directors also formed a special committee to investigate Thompson's academic credentials, as well as documents and circumstances surrounding his hiring earlier this year.

Jeff Kagan, an independent tech industry analyst, said Thompson is leaving "after a poorly handled controversy over a computer science degree.

"Yahoo has been struggling over recent years and this new incident only makes matters worse for the company," Kagan said in e-mailed comments about the Yahoo decision.