The New York Times, citing two people briefed on the matter, first reported the subpoena.
The Times says it marks the first time Mueller, who is probing Russian involvement in the 2016 election, has asked for information directly related to the Trump Organization. The action comes as the former FBI director appears to be looking into the role foreign money could have played in the president's political activities, the newspaper reported.
It is unclear exactly what information Mueller requested. Trump and his lawyers have sought a swift end to the investigation, but the subpoena indicates it could continue for at least a few more months, the Times said.
In a statement, Trump Organization lawyer Alan Futerfas said the company has cooperated with Mueller.
"Since July 2017, we have advised the public that the Trump Organization is fully cooperative with all investigations, including the Special Counsel, and is responding to their requests," he said. "This is old news and our assistance and cooperation with the various investigations remains the same today."
The Wall Street Journal, citing sources familiar with the matter, reported that the Trump Organization had been voluntarily giving documents to Mueller's office for months.
Trump has previously said he believes the special counsel investigating his finances would cross a red line. The Trump Organization has denied holding real estate in Moscow. His company considered developing a Trump Tower in Moscow in late 2015 and early 2016 before abandoning the plan, The Washington Post reported.
Earlier this month, former Trump aide Sam Nunberg said investigators wanted information about the Trump Tower plans.
Trump has repeatedly denied any wrongdoing or coordination with Russia during the 2016 election. On Thursday, White House press secretary Sarah Huckabee Sanders reiterated Trump's denial and said the president is cooperating with the investigation. She referred more specific questions to the Trump Organization.
The special counsel's office and a lawyer for Trump declined to comment to CNBC.