Michel Aoun's visit comes as the two countries are trying to establish harmonious and friendly relations. Apart from meeting Assad, Aoun will also hold talks with Syrian officials and leaders of Syria's Christian community over the next five days.
But the visit has been criticized by anti-Syrian Lebanese politicians, many of whom urged Aoun to cancel the trip. Aoun said his animosity ended when Syrian troops left Lebanon in 2005.
As acting prime minister and military commander in 1989, Aoun fought against Syrian troops in Lebanon. A year later, Syrian forces drove his troops out of their positions, forcing him into exile in France. He returned home in 2005, after Syria withdrew, ending nearly 30 years of domination of its smaller neighbor.
Later, Aoun entered an alliance with the pro-Syrian Lebanese militant group Hezbollah in its confrontation against Lebanon's Western-backed government.
"I am very happy with this visit and hope it will be the beginning of a bright period in the history of Syrian-Lebanese relations," Syria's state-run news agency, SANA, quoted Aoun as saying shortly after arrival.
After a two-hour meeting with Assad, Aoun told reporters at the presidential palace: "We spoke with open hearts and minds in order to clear the Lebanese-Syrian conscience. The person who clings to the past cannot build a future."
In the past, Aoun angered Syria when he testified against it in Washington and campaigned for the so-called Syria Accountability Act. The U.S. Congress passed the act in 2003, accusing Damascus of sponsoring terrorists and seeking weapons of mass destruction.
His visit Wednesday comes six months before Lebanon's parliamentary elections.
Aoun's showing in the 2009 vote could determine who wins a parliament majority and forms the government. It is believed that the main election battles will be in the Christian regions and over the seats he controls. His opponents contend that Christians won't back him because their mood is not pro-Syrian.
In their meeting, Aoun and Assad are also believed to have discussed the fate of Lebanese missing since Lebanon's 1975-90 civil war. The families of the missing and human rights group say Syria is holding dozens of Lebanese.