The company has 689 bookstores in 50 states as well as 674 college bookstores.
In the fiscal third quarter through Jan. 26, the New York company posted a loss of $6.1 million, or 18 cents per share. The company blamed the loss in part on charges stemming from the weaker-than-expected sales of Nook e-readers during the holiday shopping season. Analysts had expected a profit of 53 cents per share.
In the same period the year before, the New York company posted a profit of $52 million, or 71 cents per share.
Revenue fell 9 percent to $2.22 billion — analysts polled by FactSet predicted a more modest decline, to $2.4 billion.
Nook revenue fell 26 percent to $316 million. Barnes & Noble company recorded $21 million in returns due to weak demand during the holiday season, and $15 million in allowances for promotions.
"Coming off the holiday shortfall, we're in the process of making some adjustments to our strategy as we continue to pursue the exciting growth opportunities ahead for us in the consumer and digital education content markets," he said.
In a call with investors, Lynch also addressed the offer of Leonard Riggio, Barnes & Noble's founder, to buy the physical bookstores and website of Barnes & Noble, but not the Nook unit. No terms or other details have been announced.
"We can't comment further on Len Riggio's plan to make a proposal to purchase the retail business other than to confirm ongoing discussions between Len and the strategic committee of the board," Lynch said Thursday.
For fiscal 2013, the company expects revenue in stores open at least one year to fall in the low- to mid-single digit range. Revenue in stores open at least one year in its college bookstores are expected to fall by a low single digit percentage.
Shares rose $1.18, or 7.8 percent, to $16.41 during midday trading. The stock has traded between $10.45 and $26 during the past 52 weeks.