The Justice Department charged Bijan Rafiekian, aka Bijan Kian, 66, of San Juan Capistrano, California, and Kamil Ekim Alptekin, 41, of Istanbul, with acting as unregistered agents of the Turkish government and lying to the FBI over the 2016 scheme.
According to the indictment, Rafiekian and Alptekin made arrangements for the Flynn Intel Group to be indirectly paid $600,000 by the Turkish government to help turn US public and political sentiment against exiled Gulen.
The plan was developed at the height of the 2016 election campaign when Flynn was advising then-candidate Trump on foreign and security policy.
The goal, the Justice Department said, was to obtain Gulen's extradition back to Turkey, where President Recep Tayyip Erdogan had accused him of orchestrating the July 2016 coup attempt.
The deal with Flynn was approved at top levels of the Turkish government, the indictment said, with Alptekin keeping senior ministers apprised of its progress.
The indictment came one day ahead of the planned sentencing of Flynn, who was arrested last year over his secret dealings with Russian officials and Turkey.
Flynn admitted one count of lying to the FBI in a plea deal which led to him providing "substantial" information to Special Counsel Robert Mueller's investigation into Russia meddling in the 2016 election.
Flynn's work with the Turks has been known since last year, when the Wall Street Journal reported that he, Rafiekian and Alptekin met Erdogan's son-in-law Berat Albayrak and Turkish foreign minister Mevlut Cavusoglu in New York in September 2016.
At that meeting they discussed physically removing Gulen from his Pennsylvania home to Turkey without a legal extradition order.
The Journal cited former CIA director James Woolsey, who attended the same meeting and later told reporters he found the idea possibly illegal.
At the time the administration of president Barack Obama had not approved Ankara's extradition request for Gulen, and the Trump administration has also demurred on the issue.
"It's not under consideration," Trump told reporters on November 17.
But on Sunday, according to media reports, Cavusoglu said Trump recently told Erdogan that the White House is working on extraditing Gulen.