NEW YORK – America’s top CEOs are set for a once-in-a-lifetime pay bonanza.

Most of them got their annual stock compensation early last year when the stock market was at a 12-year low. And companies doled out more stock and options than usual because grants from the previous year had fallen so much in value that many people thought they’d never be worth anything.

But stock prices have generally surged ever since. Even with last week’s sharp declines, CEOs still have enormous gains on paper.

“The dirty secret of 2009 is that CEOs were sitting on more wealth by the end of the year than they had accumulated in a long time,” says David Wise, who advises boards on executive compensation for the Hay Group, a management consulting firm.

An Associated Press analysis of companies in the Standard & Poor’s 500 index shows that 85 percent of the stock options given to CEOs last year are now worth more than they were on the day they were granted.

For some, the value jumped by a factor of 10 or more. A year ago, after the stock market had collapsed, 90 percent of the options granted in 2008 were worth less than the original estimate, or were considered “underwater,” according to the AP’s analysis.

FORD STOCKS JUMP IN VALUE

Ford Motor Co. CEO Alan Mulally’s pay package illustrates this point. In March 2009, Ford granted 5 million stock options to Mulally. Using a complex formula, Ford assigned the options an estimated value of $5 million. At the time, Ford’s shares were trading at $1.96. Since then, the stock has jumped nearly sixfold, and Mulally’s options have a value on paper of about $48 million.

Mulally is also ahead on his 2008 options, which were valued at $9 million when they were granted in 2008. Now, they’re worth close to $21 million.

Mulally’s gains still exist only on paper, of course. The ultimate size of his payday will fall if Ford’s stock falters. But his gains could just as easily march even higher if Ford’s stock continues to rise. And they take the sting out of a 30 percent salary cut and the lack of a bonus. A Ford spokesman said the structure of Mulally’s compensation means most of it is aligned with the interests of shareholders.

Overall, the AP analysis found that the median 2009 pay package for chief executives at companies in the Standard & Poor’s 500 index fell by about 11 percent to $7.2 million. That followed a 7 percent decline in 2008 in median pay. The median value is the midpoint in the AP sample, meaning half of the CEOs made more and half made less.

The total doesn’t take into account the increase in value on paper of the stock and the options executives received. The median pay reflects only the value that companies must assign to stock compensation when it is initially granted.

Stock compensation in 2009 accounted for 58 percent of total pay for CEOs. Cash bonuses that CEOs received from meeting performance goals amounted to 20 percent and salaries represented 14 percent, with the rest from guaranteed cash bonuses and perks.

Other findings in the AP analysis:

No financial companies were in the AP’s top 10. Three were on the 2008 list. Citigroup Inc.’s Vikram Pandit went from No. 10 in 2008 to the third-lowest-paid CEO in the AP analysis in 2009.

The median value of performance-based cash bonuses rose 19 percent, making it the fastest-growing component of executive pay in the AP sample. CEOs generally had to meet goals for profits and stock returns in 2009 to receive the bonuses.

Some companies made that easy. In early 2009, as the stock market was still falling and the economy was in a deep recession, many companies lowered the bar on the benchmarks for profit and stock returns. As profits began to improve with the economy and the market rebounded, many executives easily beat the stripped-down goals.

CUTBACKS IN PERKS

The AP’s analysis found evidence that boards took some action amid a public outcry over executive pay following the financial meltdown and the onset of the Great Recession. The median amount CEOs received in perks fell by 15 percent in 2009, as companies cut back on benefits such as the use of corporate jets for personal travel. And fewer CEOs got a guaranteed cash bonus.

“There were deliberate efforts by companies to take away things that could get them noticed,” says J. Robert Brown, a professor of business law and corporate governance at the University of Denver and an expert on compensation issues.

Pandit’s pay for 2009 consisted of $125,001 in salary and $3,750 in 401(k) benefits. Citigroup’s board said he earned a bonus for his work in 2009, but Pandit said he won’t take one until the company returns to profitability.

His compensation in 2008 was an estimated $38 million, mainly because of a large grant of stock awards and options in January 2008 shortly after he became CEO. That stock compensation was granted when Citigroup’s stock traded around $23 a share. Today, it trades around $4 a share. Pandit still has time for Citigroup’s stock to rebound. His options don’t expire until 2018.

A few other CEOs, including General Electric Co.’s Jeffrey Immelt, turned down bonuses. United States Steel Corp. CEO John Surma took a salary cut and refused any stock compensation because of the difficult business climate.

But experts say those examples weren’t typical. “There have been gains chipping away at the sides, but the real fundamental changes still need to be made,” says Jesse Brill, chair of the website CompensationStandards.com and an expert on CEO pay.

Chief among those changes: Limiting how much wealth CEOs can accumulate through big grants of stock and options.

“The purpose of stock options was to create a nest egg that a CEO would receive after a successful career,” Brill says. “Once that number is big, there is no reason to keep adding to it. Additional grants do not provide additional motivation.”

The AP’s analysis looked at 320 companies in the S&P 500 that filed proxy statements with federal regulators between Jan. 1 and April 30 and had the same CEO for the past two years. CEOs new to the job in 2009 were included on the AP’s highest-paid list but were not used in the year-over-year analysis.

Stock market data were provided to the AP by Capital IQ, a unit of Standard & Poor’s.