A spokeswoman for the president said Mr Higgins and Mrs Clinton discussed a number of issues including their shared interest in upholding and defending global human rights and the peace process in Northern Ireland and its value as a model for resolution in regional conflicts.
"The president availed of the opportunity to thank Secretary Clinton for all her support to Ireland over the years - as First Lady, US Senator and latterly as Secretary of State," she added.
Mrs Clinton travels to Belfast on Friday after a series of events in Dublin.
However loyalist violence could mar the trip after the non-sectarian Alliance Party was targeted as a row over changes to the flying of the Union flag in Belfast escalated.
Mrs Clinton, who visited Northern Ireland three times during the 1990s with her husband, former US president Bill Clinton, plans to discuss the peace process and trilateral US-Ireland Research and Development Partnership and economic opportunities for Northern Ireland.
Elsewhere Mrs Clinton launched a new Institute for International Conflict Resolution and Reconstruction at Dublin City University, where she delivered a speech on global human rights.
She told more than 1,000 students that Egyptian people deserved a constitutional process that was open, transparent and fair. She said: "The upheaval we are seeing once again in the streets of Cairo and other cities indicates that dialogue is urgently needed.
"We call on all the stakeholders in Egypt to settle their differences through discussion and debate and not through violence. And we call on Egypt's leaders to ensure that the outcome protects the democratic promise of the revolution for all Egyptians."