Thompson came to Yahoo! by way of PayPal, a subsidiary of eBay, where he served as president, CNN reported Friday.
The Washington Post reported biographies for Thomson as far back as 2008 include reference to a degree in computer science he received from Stonehill College.
The college, however, denies Thomson was awarded a degree in computer science, where he received a degree in accounting.
The false degree was unearthed by activist investor Dan Loeb, whose company ThirdPoint owns 5.8 percent of Yahoo! shares, the Post reported.
In a letter to the Yahoo! board, Loeb declares, "A rudimentary Google search reveals a Stonehill College alumni announcement stating that Mr. Thompson's degree is in accounting only.
"That announcement is consistent with other documents (including filings with the Securities and Exchange Commission) that reflect Mr. Thompson received a degree in accounting, but not computer science," the letter to the board reads.
Bitingly, the letter says, "We learned that during Mr. Thompson's tenure at Stonehill only one such course was even offered -- Intro to Computer Science. Presumably, Mr. Thompson took that course."
Yahoo! at first called the computer science degree listed in Thompson's company biographical material as an "inadvertent error." But then it deleted references to it on company Web sites and issued a statement saying it was looking into the issue and would "make an appropriate disclosure to shareholders."