Speaking at a joint news conference, Putin focused on economic cooperation, saying there was an 80% increase in trade between the two countries last year.
He said Russia would contribute to the construction of a nuclear power plant, training staff and scientific research.
El-Sisi covered both economic and political cooperation in his remarks.
The Egyptian President said he had stressed the importance of "military cooperation" to his Russian counterpart and the continuation of "strategic relations" and high-level meetings to discuss regional issues.
He said both sides were in agreement on the importance of standing together to fight terrorism.
"I agreed with the Russian President that the terrorism challenge Egypt is facing knows no borders," he said.
The battle against terrorism isn't only on the security front, el-Sisi said, but also includes addressing the ideological and social foundation of extremism.
In discussions on regional issues, el-Sisi said he had stressed the need for a two-state solution to the Palestinian-Israeli conflict as well as threats to the sovereignty of Libya and the unity of both Iraq and Yemen.
Both leaders discussed reaching a peaceful solution to the Syrian crisis, including a meeting for all sides involved, he said.
"We agreed on the need of the world to come up with a more democratic and just system," el-Sisi said.
Putin's sole mention of political cooperation was on the subject of Syria.