During a telephone call, the White House said, Obama encouraged Sisi to "invest in the political, economic, and social aspirations of the Egyptian people."
"President Obama also expressed concern about mass trials, the status of NGOs, and the continued imprisonment of journalists and peaceful activists in Egypt," the statement said.
In early December, an Egyptian court sentenced 188 people to death for the murder of 13 police officers -- the latest in a series of mass trials launched by authorities amid a crackdown on supporters of ousted president Mohamed Morsi.
Hundreds of Morsi supporters have been sentenced to die in swift trials the United Nations has called "unprecedented in recent history."
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Egypt has also cracked down on the press, sentencing several journalists including three from international news network Al-Jazeera to lengthy prison terms.
In June, Australian Peter Greste, Egyptian-Canadian Mohamed Fadel Fahmy and Egyptian Mohamed Baher were convicted of supporting the blacklisted Muslim Brotherhood.
Since the fall of Hosni Mubarak in 2011, the United States has faced a dilemma in Egypt.
Washington regularly expresses dissatisfaction over the country's poor human rights record, but also relies on its military alliance as a centerpiece of American diplomacy in the Arab world.
During Thursday's telephone call, Obama emphasized the importance of cooperation between Washington and Cairo "to promote shared interests in counterterrorism and regional security."
"The president affirmed the United States’ continuing commitment to the strategic partnership with Egypt and emphasized the importance of bilateral cooperation," the US leader said.