The Iranian embassy in Beirut said "armed terrorists" killed a man it identified as Hessam Khoshnevis, adding that he had been involved in reconstruction work in Lebanon.
The Revolutionary Guards named the slain man as Hassan Shateri, a commander of the elite Iranian military unit, in an statement on its website that said he was killed while travelling from Damascus to Beirut.
"Commander Hassan Shateri was martyred en route from Damascus to Beirut at the hands of Zionist regime mercenaries and backers," the force's spokesman Ramezan Sherif said in the statement.
Sherif said the man was a Revolutionary Guards commander as well as the head of the Iranian Committee for the Reconstruction of Lebanon.
The embassy named him as "Hassan Shateri known as Hessam Khoshnevis".
It said he was in charge of the Iranian Committee for the Reconstruction of Lebanon set up after the devastating war in 2006 between Israel and Lebanon's Shiite Hezbollah militia, which is supported by Iran.
The embassy statement did not elaborate on the circumstances or the exact location of his death.
According to Lebanese newspaper Al-Safir, "Khoshnevis was in Syria, specifically in the (northern city of) Aleppo, to study projects to reconstruct the city".
Iran is the main regional backer of Syrian President Bashar al-Assad's regime, and has admitted Revolutionary Guards members were present in Syria playing a consultative role.