Jason Kempen for Getty Images/Craig F. Walker for the Denver Post
Steve Ells and Monty Moran made $28.9 million and $28.2 million respectively last year, the company said in a filing on Friday.
The amounts represent a 15% pay increase for each executive compared to the previous year.
Ells also raked in another $41.6 million in 2014 exercising previously awarded stock options.
The company's stock increased nearly 29% in 2014.
Shareholders have been putting pressure on Chipotle to reduce its generous compensation plan for Ells and Moran.
"At least four pay proposals are up for a vote at the company's annual meeting May 13, including one that shareholders sign off on equity compensation before awards are granted by directors," USA Today reports. "Chipotle's board is urging shareholders reject the proposals."
For comparison, Goldman Sachs CEO Lloyd Blankfein made about $23 million in 2013.
Chipotle pays workers an average of $8.57 an hour according to Glassdoor, which is a higher wage than Taco Bell, Chick-fil-A, McDonald's, Wendy's, or Burger King.