Putin will then move on to Israel for a meeting with Prime Minister Ariel Sharon.
Putin has not visited an Arab country since his election in 2000. Before his departure from Moscow, the Russian president said he hoped to restore close communication with Arab countries.
He placed an emphasis on Egypt, which was once a warm ally of the former Soviet Union and remains an important trade partner for Russia.
Yevgenii Volk, a political expert at the Heritage Foundation in Moscow, said Russia is starting to realize that it can play a greater role in the Middle East after four decades of diplomatic neglect.
"The time has come when there is a real need for Russia to rethink its policy in the Middle East -- to act on the basis of admitting equal rights for both sides; to show that Russia has a new understanding of its role and can play the role of mediator, an active role in the peace process in the Middle East," Volk said.
Putin and Mubarak are expected to discuss Iraq, Lebanon, and Syria, and attempt to stimulate the stalled peace process between Israel and the Palestinians. Russia is one of the four international mediators for the peace plan, but its role in the so-called Quartet has so far been limited.
The Soviet Union and Egypt used to enjoy close ties, but relations turned sour in the early 1970s after the newly elected President Anwar Sadat launched a pro-U.S. policy. Mubarak has maintained this policy.
The last Russian leader to hold a presidential meeting in Egypt was Nikita Khrushchev in 1964.
The Soviet Union also severed ties with Israel after the 1967 Middle East War in which Israel captured Arab territory. Relations began to warm only in 1986, when Soviet leader Mikhail Gorbachev lifted restrictions on Jewish emigration to Israel. Israel now assists Russia in antiterrorism efforts and is home to a large Russian population.
During his meeting with Putin, however, Sharon is likely to raise concerns over Russia's nuclear cooperation with Iran, as well as Moscow's decision to sell missiles to Syria. Israel believes those two countries are linked to terrorism.
Putin, on his part, might ask Israel to extradite media tycoon Vladimir Gusinskii and former Yukos executive Leonid Nevzlin, who are in self-imposed exile in Israel and wanted in Russia on various charges.
Russian political experts said they do not expect major breakthroughs during Putin's four-day tour, as Russia's influence in the Middle East remains small.
Volk, however, said the visit is an indication of Russia's desire to restore its global prestige following a series of humiliations in former Soviet countries.
"In the context of the famous failures of Russia's foreign policy in the CIS -- Georgia, Ukraine, Kyrgyzstan, partly in Moldova -- Putin is in great need of foreign policy successes," Volk said. "I think that this visit aims at showing that Russia is still strong in foreign relations."
From Israel, Putin plans to travel on to the West Bank city of Ramallah for a meeting with Palestinian leader Mahmud Abbas.