Officials said Mahmoud Ahmadinejad, on his first trip to Damascus since taking office in August, will hold talks with Bashar al-Assad, the Syrian president, and sign a number of bilateral economic cooperation agreements.
Thursday's trip comes at a time of intense pressure on Syria and Iran, caught in separate standoffs with the international community.
The US and the European Union's three biggest powers, Britain, France and Germany, said this month Iran's resumption of nuclear research meant it should be referred to the UN Security Council, which could impose sanctions.
Iran removed the UN seals on its uranium enrichment equipment but says it has no intention of building nuclear arms and seeks only a peaceful programme.
Syria also faces pressure from the council, which passed a resolution in October demanding it cooperate fully with a UN inquiry into the assassination of Rafiq al-Hariri, the former Lebanese prime minister, or risk unspecified further action.
Syria has denied any involvement in the murder but has said it will not allow investigators to question al-Assad in the case.
Ahmadinejad is also locked in a
face-off with Western powers
Neither Syria nor Iran face an imminent threat of military action or broad sanctions at the council, but will come under more diplomatic pressure on every front, analysts say.
Al-Assad has already made a point of being the first head of a foreign state to visit Iran after Ahmadinejad, a religious conservative, took office.
Iran's new president seized that opportunity to vow closer cooperation in the face of US pressure and is returning the visit at a time when al-Assad finds himself particularly isolated.