Obama and Sisi met on Thursday on the sidelines of the UN General Assembly in New York, as the two countries gingerly sought common ground after a period of turmoil caused by the toppling by Sisi, a former army chief, of Egypt's first elected president, Mohamed Morsi, last year.
Ben Rhodes, US deputy national security adviser, announced onboard Air Force One that the talks were "productive" and focused on issues wracking the Middle East, including US operations to take on the Islamic State (IS) group and counterterrorism.
Rhodes said that Obama specifically raised Washington's "ongoing concerns about Egypt's political trajectory. They had a frank exchange on those issues".
"The president raised a number of specific concerns that we have related to human rights," Rhodes said, including the rights to free speech and the rights of journalists. "The president expressed his view that those journalists should be released."
Obama had said earlier that he and Sisi intended to discuss a range of security issues, including the Israeli-Palestinian conflict, Libya and IS. The US has frequently raised the plight of three Al Jazeera journalists jailed by Egypt after being accused of ties with Islamists.
Australian Peter Greste, Egyptian-Canadian Mohamed Fahmy and Egyptian Baher Mohamed were convicted in June after being falsely accused of aiding the Muslim Brotherhood. Greste and Fahmy received seven-year terms, while Mohamed was sentenced to 10 years, in a case that caused international outrage.
Eleven defendants who were tried in absentia, including one Dutch and two British journalists, were given 10-year sentences.