Washington last week formally accused the Russian government of trying to "interfere" in the 2016 White House race.
Washington last week formally accused the Russian government of trying to "interfere" in the 2016 White House race by hacking US political institutions, charges the Kremlin has repeatedly dismissed.
However, there was no indication from Czech police that the arrest in Prague was linked to the US claims.
"Czech police have successfully collaborated with the Federal Bureau of Investigation (FBI). The aim of the operation was a Russian citizen suspected of hacking attacks on targets in the United States," police spokesman David Schon said in a statement posted on the force's website.
The arrest took place in a hotel in Prague city centre, the statement said, without identifying the man by name or indicating when the arrest took place.
The suspect collapsed in police custody, was given first aid and then hospitalised, it added.
Czech judicial authorities must now rule on his extradition to the United States, the statement said.
The Kremlin on Saturday slammed Washington for its "unprecedented" threats after US Vice President Joe Biden told NBC that Putin would receive a "message" over the alleged hacking.
Biden said Washington would respond to the alleged attacks "at the time of our choosing and under the circumstances that have the greatest impact."
NBC later reported that the CIA was preparing a retaliatory cyber attack "designed to harass and 'embarrass' the Kremlin leadership."
The Kremlin was propelled to the heart of American politics in July after Hillary Clinton's campaign blamed Russia for an embarrassing leak of emails from the Democratic National Committee.
Russia has been accused of favouring Republican candidate Donald Trump -- who has praised Putin and called for better ties with Moscow -- over the more hawkish Clinton.
Russia's relations with the United States have fallen to their post-Cold War nadir over the conflict in Ukraine and stalled efforts to end the five-year Syrian war.