Mr Mathrani, with a total compensation of $39.2 million in 2016, is overpaid by $26 million, according to the report.
Using a regression analysis that ties CEO pay to performance and other indicators such as the portion of pay that is offered in options and returns on corporate capital, 'As You Sow' has determined which CEOs are paid above and beyond their performance.
So the gap between CEO's performance to his pay is the criteria for the rankings.
The report cites Leslie Moonves, chief executive of CBS, as the most overpaid chief executive in the country. Mr Moonves earned compensation worth $56.7 million in 2016.
Marc Benioff of Salesforce ranks second on the list with a total compensation of $33.4 million.
Discovery Communication's David Zaslav comes in third with a compensation of $32.4 million.
Not only are many of the CEOs on the list overpaid, but the report argues that their companies underperformed on the S&P 500 last year, so they may also be a drag on shareholder returns.
Among the top 25 overpaid CEOs on the list, 15 were appearing on it for a second time, and 10 of them have been on the list three times.
Mr Mathrani joined General Growth Properties as the company was emerging from bankruptcy in 2010 and refocused the mall owner to high-end shopping centres.
His name has been mentioned several times as a potential candidate for a position in the Donald Trump administration. The company operates approximately 126 retail properties in 40 states. Headquartered in Chicago, General Growth Properties Inc has 1,800 employees.