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Mr Donahoe was paid $13.8m (£8.3m), including salary and bonus, in 2013, down from $29.7m a year ago.
While his basic salary rose by 2%, Mr Donahoe's annual cash incentive fell by 43% from a year earlier.
The company said that while their chief executive had performed well, the firm's financial performance "did not fully meet expectations".
EBay generated earnings of about $850m in the final quarter of last year - an increase of 13% - but its results have not been meeting expectations.
Paypal spin-off
However, the main explanation for the severity of Mr Donahoe's pay cut is his one-time award of $14.8m in performance shares in 2012, which doubled his compensation that year.
His sharp drop in pay comes amid an ongoing battle between the firm and activist shareholder Carl Icahn over its online payments business, Paypal.
Mr Icahn has called on eBay to spin off Paypal, which it acquired in 2002 for $1.5bn (£905m)
It has been a key driver of eBay's growth as an increasing number of consumers turn to online shopping, prompting increased use of online payment services.
The division accounts for nearly 40% of the firm's total revenue.
Mr Icahn, who owns more than 2% of eBay's shares, has also nominated two people to eBay's board.
However, on Monday eBay said that its board of directors "does not endorse any Icahn Group nominee or the Icahn proposal".
It also urged shareholders to vote against the nominees put forward by him.
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