"The reported amount of security expense is especially reasonable in light of the fact that Ms. Mayer does not ask the company to reimburse her private aircraft costs for business travel," Yahoo said in the updated annual report. "In addition, during 2015 Ms. Mayer faced specific security threats that we believed were credible."
The total compensation package was down 15 percent from her 2014 pay, in a year when Yahoo's stock declined more than 30 percent. But according to the report, Mayer wasn't really awarded the full compensation because Yahoo's financial performance fell short of goals.
Of the $35.98 million in pay, Mayer only realized $13.89 million, by the company's estimate. The estimate discounts Mayers' stock- and option-based compensation, which is tied to performance measures like improving "mavens": mobile, video, native and social revenue.
Yahoo has faced pressure from activist investors to sell its slowing internet business, which has been overshadowed by the company's valuable stakes in Asian technology firms Alibaba and Yahoo Japan. In a recent settlement with activists at Starboard, Yahoo added four new board directors, two of whom will join the compensation and leadership development committee, Yahoo said in a statement.
Still, the paid security detail isn't necessarily unusual: Facebook CEO Mark Zuckerberg , for instance, received $4.26 million worth of security in 2015 and $775,000 in private aircraft use, SEC filings showed.
— CNBC's Steven Kopack and Robert Hum contributed to this report.