In a statement carried by the official news agency, Khamenei appointed Brigadier General Morteza Rezai for the top post.
General Rezai was formerly the head of the IRGCs Counter-Intelligence Directorate.
Rezai replaces Brigadier General Mohammad-Baqer Zolqadr who was recently appointed as deputy Interior Minister with overall responsibility for internal security.
Zolqadr is a protégé and trusted confidant of Khamenei and has had a key role in the countrys security apparatus for years. He is also a staunch ally of President Mahmoud Ahmadinejad.
The IRGC was founded in the early days of the Islamic revolution in 1979 as an armed force loyal to Irans clerical rulers. Its commanders directly report to Supreme Leader Khamenei and their mission is to protect and propagate the Islamic revolution.
Since Ahmadinejad took office as President last year, hundreds of senior officers of the IRGC have been seconded to government ministries and state institutions to prop up the countrys civil administration as the Islamic Republic continues to defy the international community over its suspected nuclear weapons program.