Cook, who has been Apple's CEO since 2011, has seen his salary rise to $12,835,066 in 2017 from $8,747,719 previous year, according to a SEC filing from Apple on Wednesday.
After the release of the iPhone X, the USA tech giant recorded a strong net profit of 19% from a year ago to $10.7 billion in the fiscal fourth quarter to September 30.
Cook must use an Apple private jet whenever he travels, whether it is for work or pleasure. His personal air travel expenses totaled $93,109 in Apple's 2017 fiscal year, which ended in September, and is based on hourly flight charges and variable fuel charges, as well as departure and landing fees.
While executives have been criticized in the past for overzealously flying by private plane, Tim Cook now has no other option. The highest paid executive at Apple is Angela Ahrendts, who makes roughly $24,216,072.
The new policy was first implemented recently in the interest of efficiency and security based upon the company's global profile and the very visible nature of Cook's role as the CEO, says a new proxy statement for Apple shareholders released Wednesday.
In August, the iPhone maker's CEO received company stock worth $89 million after the company hit a key performance target.
Cook's personal security costs also totalled $US224,216, ($A287,702) according to the filing.
Cook's predecessor, the founder of Apple Steve Jobs had his own private jet that was gifted to him during 2000 by Apple.
This post has been updated with a clarification. The glass-sided store sits on shore of the Chicago River in the city's downtown.