The reopening of the US embassy in Havana is a symbolic step signaling the warming of ties between both countries.
John Kerry, who presided over the ceremony in Havana, is the first US Secretary of State to visit Cuba in 70 years.
The US flag was presented by the same US marines who brought it down in 1961.
Cuba reopened its embassy in Washington in July.
However, issues remain, with former Cuban leader Fidel Castro blasting the US for not lifting its trade embargo.
In an open letter on August 13, Fidel Castro said the US owed Cuba millions of dollars because of its 53-year-long embargo. The letter makes no mention of today’s reopening of the US embassy.
John Kerry described the hoisting of the flag as a “historic moment” speaking during the ceremony on August 14.
He also warned that the US would not stop pressing for political change in Cuba.
“The people of Cuba would be best served by a genuine democracy, where people are free to choose their leaders,” John Kerry told a crowd of hundreds gathered outside the embassy building.
In the past, John Kerry conceded, US policies have not led to democracy.
“Cuba’s future is for Cubans to shape,” he added.
Three retired marines who lowered the American flag for the last time on January 4, 1961, handed it over to marines to raise it once again in Havana as the American national anthem played.
Cuban leader Raul Castro and President Barack Obama agreed to restore ties in December 2014.
While trade and travel restrictions have been relaxed, the Republican-led US Congress has not lifted the trade embargo the US imposed on the communist-run island in 1960.
Cuba says the embargo – which it calls a blockade – is hugely damaging to its economy.
It says relations will be fully restored only once it is lifted.
Fidel Castro’s open letter was published in state newspaper Granma to mark his 89th birthday.
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