Iran's representative to the UN's International Atomic Energy Agency (IAEA), Ali Asghar Soltanieh, announced his resignation on Thursday without giving any reason, the Fars news agency reported.
"My mission is finished... and I return to Iran with satisfaction," said Soltanieh, who has held the post since 2005.
On August 15, new President Hassan Rowhani named Ali Akbar Salehi to head Iran's Atomic Energy Organisation as part of his team.
Salehi, who holds a doctorate in nuclear science from the Massachusetts Institute of Technology, already headed the organisation between 2009 and 2010 before taking up the post of foreign minister under former president Mahmoud Ahmadinejad.
Meanwhile, foreign ministry spokesman Abbas Araghchi was quoted by the press Thursday as saying "a new ambassador (to the IAEA) has been chosen and will be announced soon."
Western countries and Israel suspect Iran's nuclear programme is cover for a drive for a weapons capability, an ambition Tehran strongly denies.
The IAEA has been probing the programme for the past decade, and a number of international sanctions have been slapped on Tehran for its refusal to stop enriching uranium. That process can lead to producing the fissile core of an atomic weapon.
Talks between Tehran and major world powers have so far failed to yield an agreement.