The company said that Bulkeley quit to focus on his investments in other Internet companies, including QXL.com, one of Europe's leading online auction sites.
Bulkeley's resignation was effective immediately. In his place, the company named Steve Riggio, vice chairman of Barnes & Noble, as the acting CEO and vice chairman of Barnesandnoble.com.
"I am proud to have been part of the growth of this company for the last 12 months," Bulkeley said in a statement. "I believe it is clearly headed in the right direction."
Barnesandnoble.com announced last week that its fourth-quarter revenues more than tripled last year's total, reaching $81.5 million. Media Metrix ranked it as the 28th most visited Web site and the fifth most popular shopping site in November, the last month for which it has released figures.
Bulkeley also presided over the company's successful initial public offering last May, in which the company raised some $450 million. Bulkeley tried to push the company toward new products such as e-books and new services, such as next-day delivery of goods.
Despite these successes, Bulkeley's tenure has not been all positive. Barnesandnoble.com stock has sagged ever since its first day of trading, when shares closed up more than 27 percent. Shares in the company have consistently closed below its $18 offering price in recent months. Barnesandnoble.com shares closed down 62 cents today at $15.44.
Barnesandnoble.com is far outpaced in revenues and customers by chief rival Amazon.com, which announced last week that its own fourth-quarter revenues more than doubled to $650 million, and that it had acquired more than 2.5 million new customers during the quarter.
Bulkeley's tenure was also marked by a controversy involving the sale of hate literature such as Adolph Hitler's Mein Kampf in Germany.
After anti-Nazi organization Simon Weisenthal Center alerted Barnesandnoble.com last summer that such books are banned in the country, German book publishing giant Bertelsman, which owns 40 percent of the company, advised Barnesandnoble.com to cease its sales of the hate books. However, Barnesandnoble.com didn't cut off sales of the hate books in Germany until December.
But a Barnesandnoble.com spokesman said that Bulkeley was not forced out of the company, and chairman Leonard Riggio praised his efforts.
"We owe much to Jonathan Bulkeley for the leadership role he played for the past 12 months," Riggio said in a statement. "During that time, he helped build the foundation upon which the company's future will be based."