The second term congressman was leaving a coffee house in Penascola, Florida on Saturday, when he was struck in the back by the cup, which was thrown by a protester.
Around 20 demonstrators had gathered outside the venue, rallying against the right-wing politician.
Mr Gaetz was not injured during the protest.
Amanda Kondrat’yev was arrested and charged with misdemeanour battery and released on bail after paying for a $1,000 (£790) bond.
The activist was one of several people who ran against Mr Gaetz in the 2016 House of Representatives election before dropping out of the race.
It is unclear if the thrown drink was a milkshake, but similar incidents were reported in the UK, during the 2019 European elections campaign.
“Clearly it takes more than a drink to slow down our great team,” Mr Gaetz said after the alleged assault.
The pro-Trump Republican has previously caused controversy by inviting Charles Johnson, a suspected Holocaust denier, to be his guest at the State of the Union.
The anti-Muslim activist was repeatedly accosted by protesters armed with milkshakes during the campaign, as he tried to win votes while standing to be an MEP in Britain’s north-west.
Additional reporting by agencies
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