A man who identified himself of Ryan Clayton with the group America Take Action threw the flags before being escorted out of the Ohio Clock corridor.
According to Capitol Police spokeswoman Eva Malecki, Ryan Clayton, 36, was charged with unlawful conduct.
Several journalists in attendance captured the moment on video. A man dressed in a suit suddenly threw at least six flags at the president and began bellowing, "Trump is treason" and "Why are you talking about tax cuts when you should be talking about treason?"
Trump didn't flinch as the airborne flags headed his way, reacting only by giving a thumbs up. Clayton shouted at another point.
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"Why are you talking about tax cuts when you should be talking about treason?"
Trump was on Capitol Hill for a weekly policy lunch with Republican policymakers, and the expected topic of conversation was the comprehensive tax overhaul bill that the GOP has been cooking up in recent weeks.
If you visit the Americans Take Action website you immediately learn that this isn't Clayton's first stunt involving Russian flags. At the Conservative Political Action Conference in February, he spearheaded the distribution of over 1,000 Russian flags with Trump's name printed across the middle.