Seyyed Razi Mousavi was an experienced military adviser to the Islamic Revolutionary Guards Corps, the semi-official Tasnim news agency said.
It says he was killed in an air strike on the Sayyida Zeinab area south-east of Damascus.
Israel has carried out military strikes in Syria for years, against what it says are Iran-linked targets.
The strikes have increased in frequency over the past months following Hamas' attack on October 07.
Iranian forces have been present in Syria since the early stages of the Syrian civil war, where they helped support the regime of President Bashar al-Assad against widespread rebellion to his rule.
Mousavi is said to have been an aide to IRGC commander Qassem Soleimani, who was killed by the United States in 2020.
He was one of most senior IRGC operatives in Syria, according to Tasnim, and helped co-ordinate the relationship between Tehran and Damascus.
Iran's Revolutionary Guards said that Israel would pay for this crime.
There has been no immediate comment from Israel's military, which rarely discusses cross-border strikes.
Earlier this month, Iran accused Israel of killing two members of the Revolutionary Guards in Syria.
