In 2021, the median pay for employees was $68,254, Apple said, adding it had selected a new median employee for comparison due to changes in hiring and compensation.
The median pay in 2020 was $57,783 and the pay ratio was 256 times Cook's salary.
The iPhone maker has benefited from strong demand over the past two years as consumers working from home splurged on upgrades. Apple's revenue rose more than 30% to $365.82 billion for its fiscal 2021 and its shares briefly crossed $3 trillion in market capitalization this year.
Cook, whose salary remained at $3 million, received $82.3 million in stock awards, $12 million for hitting Apple's targets and $1.4 million for air travel, 401(k) plan, insurance premiums and others.
In total, he earned $98.7 million, compared with $14.8 million in 2020.
Cook took the helm in August 2011 after the company's co-founder Steve Jobs stepped down months before his demise. The stock has surged over 1,000% since Cook took charge.
In September, Cook received 333,987 restricted stock units, in his first stock grant since 2011 as part of a long-term equity plan. He will be eligible to receive additional units in 2023.
Cook told Fortune magazine in 2015 that he plans to donate his wealth to charity.
CEOs in the United States were paid 351 times more than the typical worker in 2020, a report by the Economic Policy Institute showed, while the compensation of top CEOs grew roughly 60% faster than the stock market from 1978 to 2020, eclipsing the slow 18% growth in a typical worker's annual pay.
(Reporting by Nivedita Balu in Bengaluru; Editing by Krishna Chandra Eluri and Devika Syamnath)