This is the Senate Foreign Relations Committee chairman's third visit to Damascus during Obama's term as president, and Kerry's fifth visit to the Syrian capital as senator.
The meeting with Assad was held not long after Obama renewed sanctions against Syria and after Washington accused Damascus of transferring missiles to Hezbollah. This appears to be the reason Kerry traveled to Damascus.
The Americans are unsatisfied with the Syrians' conduct, but continue to talk to them. Fred Jones, a spokesman for the Senate Foreign Relations Committee, said Kerry planned to discuss "regional issues" with Assad.
Kerry clarified that "while the United States has serious, long-standing disagreements with Syria, in particular its support for Hezbollah and other terrorist groups, Syria can play a critical role in bringing peace and stability if it makes the strategic decision to do so."
In the past, Senator Kerry demonstrated his special diplomatic capabilities in Afghanistan, when he succeeded in preventing a serious crisis in the relations between the Obama administration and President Hamid Karzai.
On the Syrian front, Kerry managed to create trust with President Assad, and became the administration's emissary for special missions in Damascus.
Follow-up meeting ahead of envoy's return
Kerry's first visit to Damascus was aimed at advancing mutual activities to stop terrorists from crossing from Syria to Iraq. On his second visit, the senator tried to look into the chances of advancing the Middle East peace process.
According to a source at the American embassy in Damascus, "This visit is a follow-up to previous trips that he has made to Syria."
The Obama administration committed to reappointing a US ambassador to Syria, in order to be able to relay messages on higher ranks from the American administration to the Assad regime.
Obama named Robert Ford as the ambassador to Syria in February, but despite the Democratic majority in the Senate, the appointment has yet to be voted on.
Former US President George W. Bush recalled the American ambassador following the murder of former Lebanese Prime Minister Rafik Hariri in Beirut in 2005. The Republicans object to the appointment of an ambassador to Syria, viewing it as a reward to Damascus.
Obama wants an ambassador who will be able to relay the American stand to the Syrian regime even during tough times in the relations between the two countries.
AFP contributed to this report