After meeting President Nayib Bukele on a visit to the Central American country, Rubio said the US was "profoundly grateful", adding that "no country's ever made an offer of friendship such as this".
El Salvador will also accept for deportation migrants of any nationality who are criminals and in the US unlawfully, the secretary of state said.
Rubio has praised Bukele for his policies on gang violence which have dramatically reduced crime rates in El Salvador - once the murder capital of the world - but have been criticised by human rights groups.
Rubio told reporters: "He has offered to house in his jails dangerous American criminals in custody in our country, including those with US citizenship and legal residency."
"We are profoundly grateful. I spoke to President Trump about this earlier today," he said.
Rubio is on his first overseas tour as the US top diplomat, and has been seeking to assert the Trump administration's priorities in the region, including demanding that Panama make "immediate changes" to what he calls the "influence and control" of China over the Panama Canal.
Rubio said Bukele was willing to take back citizens from El Salvador as well as migrants from other countries, and appeared to suggest the focus would be on Latin American gang members - such as MS-13 or Tren de Aragua.
Since his return to the White House, President Donald Trump has focused on speeding up the removal of unlawful migrants, with the promise of "mass deportations".
In allied moves, more active duty troops have been sent to fortify the US-Mexico border and the president has sought to halt the processing of migrants and asylum seekers via an executive order.
AzVision.az
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