Donahoe's compensation was valued at $16.5 million in 2011, according to a filing with the Securities and Exchange Commission on Monday.
His salary grew about 3 percent to $970,353.
The bulk of the pay increase came from stock awards amounting to $23.7 million last year, up from $8.9 million in 2011.
Those awards included a one-time $14.9 million grant as part of the company's performance-based incentive plan. It is structured "so Mr. Donahoe is incentivized to maintain strong performance through the vesting date of the grant in 2017," eBay spokesman John Pluhowski said.
He also got an incentive payment of $2.8 million and options worth $2 million.
EBay, based in San Jose, Calif., has been trying to expand PayPal, still largely an online payments service, into brick-and-mortar retailers. Stronger-than-expected results in the final quarter of the year topped the biggest year ever for the company.