The micro-blogging website said it did not intend to hire a replacement for Rowghani, whose operating responsibilities would be assumed by others in the management.
Rowghani, however, would continue to be an employee of the company and act as a strategic adviser to the Chief Executive Officer Dick Costolo.
Twitter says its chief operating officer, Ali Rowghani, has resigned from his post but will stay with the company as a strategic adviser to CEO Dick Costolo.
Rowghani joined Twitter in 2010 as chief financial officer and became COO two years later. Before that, he served as CFO at Pixar Animation Studios.
The San Francisco-based social media company has been trying to broaden its user base, most recently by luring in World Cup fans who want to follow teams and players using its service.
Technology news website Re/code reported on Wednesday that Twitter was considering a shake-up in its top management, including a possible shift in the duties of Rowghani.
Chloe Sladden, Twitter's North America media head, who reports to Rowghani, has been reorganizing her unit and she may be preparing to leave the company, the website added.
Twitter did not comment on Sladden in its filing on Thursday.
Twitter's first-quarter results in April revealed slowing momentum at the company that exuberant investors just six months ago had argued could one day match Facebook's scale. At the same time, Twitter estimated the monthly active users at 255 million, which led to a slump in its share price because it suggested sluggish growth.
Twitter's shares were little changed at $35.64 on the New York Stock Exchange on Thursday.
Last month, research firm eMarketer said Twitter is seeing strong user growth in the Asia-Pacific region, helping the messaging platform compensate for a slowdown in the US and Europe.
Written with agency inputs