The closed-door Capitol Hill appearance comes amid turbulence at the White House, and mounting intrigue over Special Counsel Robert Mueller's investigation into Russian interference in the 2016 election and possible contacts between Trump's presidential campaign and Moscow.
Comey smiled as he walked past reporters towards a House meeting room, telling them "maybe later" he would answer questions.
Trump's bete noire had pleaded for a public hearing after he was subpoenaed by members of the outgoing Congress in November, but House Republicans including some of Trump's allies insisted on a private session before the judiciary and oversight committees.
Flynn, who was indicted for lying to investigators, has been cooperating with Mueller's probe.
The president has repeatedly blasted Mueller's probe as a "witch hunt," and on Friday unleashed a Twitter tirade against Mueller, Comey and several other current and former officials tied to the Russia probe.
Comey is expected to be questioned as part of a Republican-led House inquiry into possible Russian interference and email use by Hillary Clinton, the Democrat who lost to Trump in the 2016 election.
It will likely be one of the last sessions conducted by the joint judiciary and oversight panel this year. Control of Congress shifts in January to Democrats, who are keen to end or alter the probe.
Comey had resisted answering questions privately, filing a legal challenge to force more transparency.
This week he said an agreement had been struck.
"Will sit in the dark, but Republicans agree I'm free to talk when done and transcript released in 24 hours," he tweeted.
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