Cook, who took the helm of the iPhone and iPad maker in August last year, two months before the death of founder Steve Jobs, clocked in total compensation of $378 million.
Cook earned $900,000 for his annual salary and $900,000 for his annual incentives.
But he scooped up a cool $376 million in restricted stock grants, based on Apple's stock price at the time.
Another Silicon Valley big gun, the head of Oracle, Larry Ellison, came in second place with less than a fifth of Cook's pay, at $76 million.
The study, conducted by Hay Group for the Journal covered the 300 largest US public companies by revenue.
Television broadcaster CBS head Leslie Moonves was in number-three position at $69 million, followed by the chief executive of struggling retailer JCPenney, Ronald Johnson, who pulled in $53 million.
Motorola Mobility chief Sanjay Jha was ranked fifth, at $47 million.
The remainder of the top 10, in descending order, were the CEOs of Citigroup, Viacom, Motorola Solutions, Walt Disney, and Ford Motor, whose Alan Mulally earned $29 million.
Apple's Cook could see his compensation climb further into the stratosphere this year. Apple shares have leaped 29 percent in the year to date, and on Monday were up 5.5 percent in late New York trade.