The New York Yankees were hit with a $13.9 million luxury tax bill Thursday, their lowest since 2003.

The fee, assessed by Major League Baseball under its labor contract, is down from $18 million last year and $25.7 million in 2009, when the Yankees won the World Series.

Boston, which missed the playoffs for the second straight season, is the only other team that will have to pay a tax. The Red Sox received a bill for $3.4 million, up from last year’s $1.5 million.

Season-ending payroll information and the tax was sent to teams and obtained by The Associated Press.

According to the collective bargaining agreement, checks to pay the tax must be sent to the commissioner’s office by Jan. 31.

New York has paid the tax in all nine years since it began, $206 million of the $227 million raised under the penalty for high payrolls. The only other teams to pay have been the Red Sox (a total of $18.8 million), Detroit ($1.3 million) and the Los Angeles Angels ($927,000).

The Yankees pay at a 40 percent rate on the amount of their payroll over $178 million, a figure that includes the average annual values of contracts plus benefits. Boston, which exceeded the threshold for the second straight year, pays at a 30 percent rate. For purposes of the tax, New York’s final payroll was $212.7 million and Boston’s was $189.4 million.

Under the new labor contract, the Yankees’ rate would increase to 42.5 percent next year and 50 percent in 2013 if they continue to exceed the threshold, and Boston’s rate would go up to 40 percent next season.

But if in any year a team goes under the threshold, its rate decreases to 17.5 percent the next time it pays the tax.

As an added incentive for the high-spenders to decrease payroll, if they get under the threshold they will become eligible to get back some of the money they contribute in revenue sharing. The tax threshold stays at $178 million through 2013, then goes to $189 million in each of the following three years.