No British royal has been to Iran for more than 32 years since the ousting of the imperial regime by the Islamic revolution of 1979.
Charles's father Prince Philip and sister Princess Anne were there in 1971 for celebrations marking the 2500th anniversary of the Persian empire.
The prince was leaving later on Monday for Bam, the historic city in southwest Iran that was devastated by an earthquake on 26 December with the loss of about 43,000 lives.
British sources insist his visit is in his capacity as head of the British Red Cross and has no political significance.
Prince Charles flew in late on Sunday from neighbouring Iraq, where he had made a surprise visit to British troops based in the south of the country.
In Bam, he was due to meet with survivors of a catastrophe that also dealt a devastating blow to world heritage. The visit has been subject to intricate security preparations and tight secrecy.
The southeastern city of Bam was
levelled on 26 December
But despite the security obstacles and political complications surrounding a visit to Islamic Iran - whose clerical regime is currently celebrating the 25th anniversary of the overthrow of the Iranian monarchy - the prince's aides said Charles has been determined to see a visit go ahead.
Bam, which had a population of some 100,000 people, was almost totally destroyed by the December quake. As well as those killed, tens of thousands of others were injured and left homeless.
Among the casualties was Bam's ancient mud-brick citadel, whose origins date back more than 2000 years and is a world cultural heritage site.
During his brief tour there of several hours, Charles will meet local farmers trying to rebuild the qanat - or ancient underground irrigation structures - and resume the growing of dates that the area is famed for.