The US citizen, a 21-year-old who reportedly worked for an American cultural centre in the coastal city of Alexandria, was killed as he took photographs of a demonstration, officials said.
"We can confirm that a US citizen was killed in Alexandria, Egypt," US state department spokesman Patrick Ventrell said in a statement.
Another man was killed earlier during the clashes in Alexandria.
In the canal city of Port Said, an Egyptian journalist was killed and several others injured after someone threw a small explosive device at anti-Morsi protesters, a security official and witnesses said.
Clashes also erupted in the Nile Delta provinces of Daqahliya and Beheira, and across the country over 130 people were wounded, security officials said.
The offices of the Freedom and Justice Party (FJP), the political arm of Morsi's Muslim Brotherhood, were torched in Alexandria and at Aga in Daqahliya, and its offices were stormed in Beheira.
The skirmishes are seen as a prelude to mass anti-Morsi protests planned for Sunday, the anniversary of his turbulent maiden year in office as Egypt's first democratically elected president.
Morsi, 62, has been accused by opponents of failing the 2011 revolution that brought him to power and of ignoring nearly half of the electorate of around 50 million who did not vote for him last year.
Sunday's protest has been called by Tamarod (Arabic for Rebellion), a grassroots movement which says it has more than 15 million signatures for a petition demanding Morsi's resignation and a snap election.
Friday's pro-Morsi demonstrations were seen as a preemptive strike by the regime ahead of the opposition rallies.
In Cairo, tens of thousands of Islamists gathered under the slogan "legitimacy is a red line," referring to Morsi's insistence that he has a popular mandate.
"We will not allow a coup against the president," senior Brotherhood leader Mohamed al-Beltagui told the crowd.
Anti-Morsi protesters joined hundreds camped overnight in Tahrir Square, epicentre of the 2011 revolt that toppled Hosni Mubarak and catapulted the Islamist to the presidency.
Opponents also gathered in Alexandria, Mansura and Port Said.
"It's not about sacking Morsi himself," one Tahrir protester told AFP.
"If any other does the same he will be sacked as well. Our demands are clear: bread, freedom, social justice and human dignity."
The unrest during Friday's rival rallies raised fears of wider and bloodier violence on Sunday's first anniversary of the Islamist leader's inauguration.
The United States called for calm.
"We urge all parties to refrain from violence and express their views peacefully," US State Department spokesman Patrick Ventrell said.
"And political leaders have the responsibility of taking steps to ensure that groups do not resort to violence."
In "our opinion, all Egyptians have the right to express their opinions and concerns freely. We've urged the government to protect that right."
Later Friday, the State Department updated its travel warning, saying non-emergency diplomatic staff could leave Egypt and warning US citizens to postpone non-essential travel to the country.
Germany warned that Egypt's fledgling democracy faced a "moment of truth", and urged Morsi to implement reforms.
At least four people have also died since Wednesday in clashes in the Nile Delta -- three in Mansura city and one in Zagazig, medics said.
Egypt is deeply split between Morsi's Islamist allies and an opposition of leftists, liberals, Christians and some Muslim groups.
Morsi warned in a televised speech Wednesday that the growing polarisation threatened to "paralyse" Egypt, pledging to consider constitutional reforms and appealed to the opposition to join talks.
On Thursday however, the opposition National Salvation Front coalition rejected his offer of talks and renewed its call for a snap presidential election.
The broad-based opposition accuses him of having hijacked the revolution.
They say he has reneged on his promise to be a president for all Egyptians and failed to deliver on the uprising's aspirations for freedom and social justice.
Since taking office last June 30, Morsi has squared off against the judiciary, police and artists.
But he has also admitted to failings.
"I have made many mistakes, there is no question. Mistakes can happen, but they need to be corrected," he said.
Amnesty International called on the authorities to ensure the security forces showed restraint and protected peaceful demonstrators from violence over the weekend.
"They should make clear that anyone responsible for arbitrary and abusive force will be brought to justice," Hassiba Hadj Sahraoui, Amnesty's Middle East deputy director said in a statement Friday.
The army, which oversaw the transition from Mubarak's autocratic rule but has been on the sidelines since Morsi's election, has warned it would intervene in the event of violence.