Pence and El-Sissi held 2½ hours of talks at the presidential palace in Cairo, with acknowledgements of friendship and partnership between the two countries. Through a translator, Pence listened intently as el-Sissi cited the need to address "urgent issues," including "ways to eliminate this disease and cancer that has terrified the whole world."
Pence pointed to President Donald Trump's efforts to forge stronger ties with el-Sissi in his first year in office, "after a time when our countries seemed to be drifting apart."
Pence said "we stand shoulder to shoulder with you and Egypt in fighting against terrorism," and that "our hearts grieve" for the loss of life in recent terrorist attacks against Egyptians.
The vice president noted the deadly attack against Christians in late December, when a militant opened fire outside a suburban Cairo church, killing at least nine people. He also pointed to the killing of 311 worshippers inside a mosque in northern Sinai last November.
"We resolve to continue to stand with Egypt in the battle against terrorism," Pence said.
Pence arrived in Cairo hours after the US Congress and Trump failed to reach agreement on a plan to avert a partial federal closure. Pence went ahead with his four-day trip to the Middle East, citing national security and diplomatic reasons.
Pence's meetings with El-Sissi delved into security cooperation, economic ties and efforts to fight Daesh.
His visit to the region came more than a month after Trump announced his decision to recognize Jerusalem as Israel's capital, a step that's enraged Palestinians. El-Sissi identified "the peace issue" as one of the most important issues in their discussions, but the two leaders did not elaborate.
When Pence's motorcade arrived at the palace, journalists traveling with the vice president were initially barred from exiting their bus. After they were brought into the palace, media were not allowed into a photo session with the two leaders. Negotiations between US and Egyptian officials followed, and members of the media were eventually were brought into the meeting and heard the leaders deliver short statements.
Pence and El-Sissi did not respond to questions at the end.
Pence planned to travel to Jordan later Saturday and then to Israel on Sunday. He was not expected to meet with Palestinians officials.
El-Sissi has built a strategic alliance with Trump and urged the American president to become more involved in the fight against Islamic militancy in the Middle East. Trump has praised el-Sissi for the April release of Egyptian-American charity worker Aya Hijazi, who had been detained for nearly three years.
But Trump's designation of Jerusalem as Israel's capital poses a dilemma for Egypt, which receives extensive military and economic aid from Washington but does not want to appear dismissive of Palestinian concerns.
White House officials said before the Cairo meeting they expected the decision on the Israeli capital and Trump's plans to move the US Embassy from Tel Aviv to Jerusalem to come up.
Palestinian leader Mahmoud Abbas has condemned Trump over the Jerusalem announcement and warned that the US can no longer play any role in future peace negotiations between the Palestinians and the Israelis.
El-Sissi has tried to reassure Abbas of his continued efforts to secure an independent Palestinian state with east Jerusalem as its capital.
The Egyptian leader, who led the 2013 military overthrow of an Islamist president, has announced plans to run in the March election. El-Sissi is heavily favored to win a second four-year term after leading a heavy crackdown on dissent, jailing thousands of opponents, including many of those behind the 2011 uprising that toppled Hosni Mubarak.
White House aides said Pence was expected to raise with el-Sissi the importance of human rights, political freedoms and freedom of expression.
Pence had initially planned to visit the region in December, shortly after Trump's announcement, but the trip was postponed in the aftermath of Abbas' refusal to meet the vice president in Bethlehem.
The spiritual leaders of Egypt's Muslims and Orthodox Christians also canceled their meetings with Pence.