In 1989, Ellian came to the Netherlands as a political refugee. Having experienced first-hand the Islamic theocratic government of Iran, he writes often about how such issues are affecting the world and the Netherlands in particular. Due to threats on his life tied to such criticism, he is currently heavily guarded.
Ellian grew up in Iran.As a youngster, he was a journalist for Iranian political magazines aimed at youth. Three years after the Iranian Revolution in 1979, the communist Tudeh Party that he belonged to was outlawed, and Ellian was in danger of being arrested. He decided to escape to Pakistan. However, there he still faced extradition back to Iran so shortly afterwards he fled to Soviet-occupied Afghanistan. There he studied medicine in Kabul and met his wife.
After five years in 1989, at the same time the Soviets retreated from Afghanistan, according to Ellian he was invited to come to the Netherlands and was flown out of the country by the United Nations together with other dissidents, who feared extradition to Iran. Dutch author Ian Buruma wrote in his book Murder in Amsterdam: The Death of Theo Van Gogh and the Limits of Tolerance (2006) that his flight from Afghanistan was "as bogus as Ayaan's refugee story", because he pretended to be an "East-European-style dissident" (page 156). A Dutch television documentary programme in 2006 exposed that politician Ayaan Hirsi Ali had lied in her claim for asylum, which led to her resignation from parliament.
In the Netherlands Ellian started his studies of law at the Catholic University of Brabant (now the University of Tilburg). In 1996, he graduated with a degree in civil law, criminal law, and philosophy.He remained in Brabant as a researcher until he found a position with the Amsterdam Center for International Law, of the University of Amsterdam. He would obtain a PhD from the University of Tilburg in 2003, on the subject of the South African Truth and Reconciliation Commission, where he focused on the tension between criminal law and reconciliation. He concluded that the commission was an acceptable tribunal worthy of international respect. Since November 1, 2003, he has been professor of law at the University of Leiden.
Ellian was a regular columnist for NRC Handelsblad, and makes appearances on political discussion programs on Dutch television. At first together with writer and columnist Leon de Winter, Ellian writes blog articles for the magazine Elsevier. He was also an advisor to the Committee for ex-Muslims, which has ceased to exist.
Following the 2009 Iranian presidential election, Ellian wrote an open letter to Ali Khamenei, the Supreme Leader of Iran. The letter was published by German magazine Der Spiegel and Dutch newspaper NRC Handelsblad. Der Spiegel subtitled the letter "Your Regime Is Finished" (not a direct quote from Ellian), while NRC Handelsblad subtitled it "The children of the revolution will accept the ayatollah's rule no more.