Apple has the biggest market value of any tech company, so it’s no surprise that Apple chief executive Tim Cook has become the highest-paid CEO at a publicly traded company in the San Francisco Bay Area.

Cook beat out Larry Ellison ($77.5 million) of Oracle for the title, bringing in $378 million in his first year as Apple’s boss, according to an analysis by the San Jose Mercury News. The pay was mostly in shares that Cook won’t be able to sell for years. Cook’s actual take-home pay was $1.8 million.

The median pay for Bay Area CEOs was $3 million, according to the San Jose Mercury News’ What the Boss Makes annual survey. That number was up from $2.8 million in 2010. The survey includes salaries, bonuses, stock grants, and options reported by 198 publicly traded companies in the fiscal year 2011.

Third place was John Hammergren, CEO of healthcare firm McKesson, at $32 million. John Daane of Altera got $29.6 million, and Chevron’s John Watson got $18.1 million. Meg Whitman of HP got $16.5 million, while the previous CEO, Leo Apotheker, got $13.2 million after he was fired.

Former PG&E CEO Peter Darbee got a $34.8 million retirement package, even after he left the company in the wake of a deadly gas line explosion in San Bruno, Calif. Carol Bartz, former Yahoo CEO, got $3 million in severance, while AMD’s former CEO Dirk Meyer got $8.7 million.

VentureBeat's mission is to be a digital town square for technical decision-makers to gain knowledge about transformative enterprise technology and transact. Discover our Briefings.