The ministry said Hassan Irloo was in need of urgent medical care after being infected for several days, and was on his way to Iran.
“In order to transfer him to our country for treatment, the Foreign Ministry conducted consultations with some regional countries to prepare for his transfer, which is currently under way,” ministry spokesman Saeed Khatibzadeh told state media.
Mr Irloo was appointed by Tehran in October last year as its ambassador to Sanaa, but stands accused by the US government of being a member of the radical Islamic Revolutionary Guard Corps.
He predecessor left Sanaa in September 2015. In October 2019, Iran said the process of sending a new ambassador had been hindered by “attacks on the embassy”.
Yemen has been mired in violence since the Houthis ousted the internationally recognised government from Sanaa in late 2014.
The departure of the Iranian envoy follows the return of another senior figure from the regime to Tehran. On November 11, Iran's Tasnim News Agency reported that Gen Javad Ghaffari of the IRGC had left Syria.
Gen Ghaffari played a leading role in Iranian military advisory efforts to assist President Bashar Al Assad during the height of Syria's civil war.
This prompted speculation that a rift may have emerged between the Syrian government and the IRGC following the proliferation of Iran-backed militias in the country, with many units composed of Iraqi and Afghan recruits.
Iran’s Foreign Ministry spokesman denied that Gen Ghaffari had been expelled however, instead saying that his departure marked the end of a “successful mission”.