Thompson, outgoing director-general of the British Broadcasting Corp, will receive a compensation package that includes $1 million in an annual base salary, plus bonuses and $3 million in performance-based stock and stock options.
His compensation is similar to that of former New York Times CEO Janet Robinson, except that Thompson will not take part in the company's pension plan.
Thompson will also receive up to $60,000 in relocation fees to New York from Oxford, England, and $25,000 in legal fees connected with the employment agreement, the company said in the filing with theSecurities and Exchange Commission.
The New York Times named Thompson CEO on Tuesday, capping an eight-month search for a CEO. He starts in November.
Robinson left abruptly last year after a 28-year career with the Times Co. She received a total payout of $24 million.
Times Co Chairman Arthur Sulzberger Jr. received $5.9 million in total compensation in 2011.
Shares of the New York Times Co were up 0.5 per cent at $9.44 in morning New York Stock Exchange trading.
Copyright @ Thomson Reuters 2012