The move marks the latest deterioration in relations between Washington and Havana since US President Donald Trump entered office in 2017.
Washington's Deputy Chief of Mission at its embassy in Havana, Mara Tekach, said in a video published on social media that the measure was taken because "US immigration law requires that US visa fees and validity periods be reciprocal."
She said Cuba allows US tourists a single entry visa valid for up to three months.
The new US rules apply to Cubans seeking to visit the US for family visits and medical treatment as well as vacations.
The measure comes into effect on March 18 but won't affect existing visas, a Department of State official said.
Under Obama, US-Cuba relations thawed after decades of tension, with the two countries reopening embassies in each other's capitals.
But under Trump, Washington has ramped up sanctions, first applied in 1962, against Cuba's communist regime.
Trump has hit out at Cuba over its support for its socialist ally, Venezuela's President Nicolas Maduro, while he also claimed last month that leftist ideologies in the region were "dying."
The US evacuated diplomatic staff and their families in 2017 after at least two dozen people suffered brain injuries that resembled concussion, but with no exterior signs of trauma.
The US accused Cuba of carrying out "health attacks" using some sort of acoustic or microwave device, a charge Havana angrily rejected.
Cuba insisted the move was "politically motivated."
Friday's announcement will make it even harder for Cubans to gain US visas: they already have to travel abroad to apply due to the lack of US consular services on the island nation.
Even so, of the two million Cubans living outside the country, most reside in the US.
The US government does not allow its citizens to travel to Cuba as tourists, likewise meaning that travelers must leave the country before applying for a visa to visit the Caribbean island.