The loss at the company, which announced more than 100 editorial job cuts earlier this week, included a one-time $76.1m charge relating to pensions at The Boston Globe.
Revenues were down 17% percent to $570.6m, which was ahead of forecasts predicting $561.6m, according to Thomson Reuters.
It reported a loss per share of $.25 compared with $.80 per share in the third quarter of 2008. Earnings per share excluding severance and special items were $.16 per share compared with $.05 per share last time.
Janet Robinson, president and CEO, said: "Our third-quarter results reflect the positive benefits of the sustained actions we have been aggressively pursuing to reposition our businesses for the evolving future of the media industry."
Looking ahead Robinson said that visibility remained limited for advertising in the fourth quarter, but said the New York Times was seeing encouraging signs of improvement in the overall economy and in discussions with our advertisers.
"Early in the fourth quarter, print advertising trends, in comparison to the third quarter, have improved modestly, while digital advertising trends are improving more significantly."
Robinson confirmed that following its decision not to sell the Boston Globe it was moving ahead with its potential sale of its interest in New England Sports Ventures, which includes the Boston Red Sox baseball club and New England Sports Network.
At the New York Times Media Group, which includes The New York Times and The International Herald Tribune, circulation revenue hit $175.2m while advertising revenue dropped to $164.5m.
The New York Times Co results were in line with rivals including USA Today owner Gannett and The Miami Herald McClatchy Company.
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