Mr Cook's salary rose to $2m (Â£1.3m) from $1.4m, and his total remuneration more than doubled to $9.2m in 2014.
The base salaries for other executives were also increased by over 14% to $1m, the company said in its annual report.
Apple's New York-listed shares had hit a record high last year, while almost 40m iPhones were sold.
The increase to Mr Cook's salary was the first since November 2011. He became chief executive in August that year following the death of Steve Jobs.
In the report, Apple said the increases were given after reviewing data provided by its independent compensation consultant about the arrangements of its competitors.
The executive team's bonuses were also increased to a maximum of 400% of the member's salary.
In November, Apple was worth more than $700bn after its stock hit a record high of $119.75. The stock was trading at $112.29 in New York on Friday, valuing the company at $658bn.
Angela Ahrendts, the former Burberry chief executive who joined Apple last year in the newly created role of senior vice-president, retail and online stores, was awarded a bumper package worth just over $73m (Â£48.6m).
The total included share options worth $37m to compensate for those she lost by leaving Burberry, along with $33m given as a "golden hello".
Ahrendts' base salary was $1m, and she was also paid a $1.6m cash bonus and a hiring bonus of $500,000.
Total compensation for Luca Maestri, Apple's chief financial officer, topped $14m - also exceeding Mr Cook by a substantial margin.
However, Mr Cook was awarded a pay package worth $378m when he took the top job - mostly comprised of share options that he will receive in 2016 and 2021.
Meanwhile, Apple said that Millard "Mickey" Drexler, who has been a director on its board since 1999, will step down in March.
The former boss of Gap and chief executive of J Crew was a close ally of Mr Jobs and was credited with Apple's push into opening its own retail stores.
Drexler's replacement has not yet been announced.
The base salary of Apple chief executive Tim Cook was increased by almost 43% in February last year, according to the technology giant.