Apple reported that Mr Cook's personal travel expenses came to $93,109 (£69,253) in 2017.
The world's most valuable company requires its chief executive to use private aircraft for all business and personal travel as an "additional security measure", according to the company's most recent regulatory filing.
The bumper package is linked to Apple's share price performance versus its S&P 500 peers and comes after the company beat its annual sales and income targets.
"This policy was implemented in 2017 in the interests of security and efficiency based on our global profile and the highly visible nature of Mr. Cook's role as CEO", says Apple in a new shareholder proxy statement released on Wednesday afternoon.
For the company's 2017 fiscal year ended September 30, Apple reported sales of $229.2 billion (up 6.3% from the year prior) and net income of $48.4 billion (up 5.8%).
Cook's personal security costs also totalled US$224,216, ($316,357) according to the filing. Iger's personal air travel expenses totaled $282,831 in fiscal 2016, while the Facebook chief executive racked up about $871,390 in costs related to personal usage of private planes previous year.
"Apple was above its target performance goals for both net sales and operating income, resulting in a payout of each named executive officer's annual cash incentive", the company's filing said.
However, Cook is also sitting on a pile of Apple stock.
Cook's "top five lieutenants", as Bloomberg calls them received compensation totaling $24.2 million the year.
In 2014, executives including Dan Riccio, chief of hardware engineering, and former General Counsel Bruce Sewell received performance awards that paid out three years later at nearly twice as many target shares as planned after Apple's stock returned 69 percent over that span, including reinvested dividends.
The article previously stated Tim Cook received a private plane when he actually received the use of a private aircraft.