Cook, the successor to the late Steve Jobs, was awarded total compensation of $4.17 million in 2012, down from $378 million in 2011, Apple said in a federal filing on Thursday.
The 2012 compensation package for Cook, who took over as chief executive in August 2011, also seemed a pittance compared with his 2010 pay, which was 14 times higher, when the executive served as chief operating officer.
Jobs, the iconic CEO and co-founder, died in October 2011 of pancreatic cancer.
The maker of the iPhone and iPad noted that Cook will not receive any stock awards for 2012 after he was given about $376.2 million in stock awards the year before. The stock awards vest over many years.
The 2012 package includes a salary of $1.4 million and a nonequity bonus of $2.8 million, according to the filing. Cook's base salary actually increased compared with the $900,000 he earned in 2011.
While Apple's shares are 35 percent higher than when Cook assumed the CEO role, they have fallen more than 27 percent since October when they hit a $700.10 high.
Apple shares were down 0.6 percent at $509.85 on the Nasdaq late on Thursday morning.