He was forced to resign in February after failing to disclose the content of his talks with Russian diplomats.
Meanwhile, the fallout continues over the firing of the FBI director.
The White House maintained that James Comey was removed on Tuesday for his handling of the inquiry over Hillary Clinton's emails.
But senior Democrats said they believed he had recently asked the justice department for more resources for his Trump-Russia investigation.
Flynn: Documents demanded
The Senate Intelligence Committee said it issued a subpoena after Mr Flynn rejected its request on 28 April to submit documents relevant to the investigation.
Mr Flynn, a retired army lieutenant-general, misled the White House about discussing US sanctions against Russia with the country's envoy, Sergei Kislyak, before Donald Trump's inauguration in January.
His links to Russia are being scrutinised by the FBI and the House and Senate Intelligence Committees, as part of wider investigations into claims Moscow sought to tip the election in favour of Mr Trump, and into contacts between Russia and members of the president's campaign team.
The rare use of a subpoena by senators makes it clear that the committee is forging ahead with its investigation into the alleged Trump-Russia links, the BBC's Laura Bicker in Washington says.
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