Ramadan "continued to participate in this programme even after the elections in Iran, when authorities there hard-handedly stifled the freedom of expression", the City of Rotterdam and Erasmus University said in a joint statement.
It said Ramadan had "failed to sufficiently realise the feelings that participation in this television programme, which is supported by the Iranian government, might provoke in Rotterdam and beyond".
He had worked at the university since 2007.
Ramadan - known as a reformist who condemns terrorism and urges Muslims living in Europe to integrate - has recently been criticised in the Dutch press for allegedly voicing more conservative views for Muslim audiences than he does in the West.
In response, Ramadan has written an open letter to Dutch media saying that the show was a debate forum, and that he had no involvement with Iran's government.
"Repression against and killing of civilian people cannot be accepted and must be condemned," he said in the letter, published by Dutch media last week when the debate broke out.
"I support transparent, democratic process, and I expect the Iranian regime to respect this principle."
Ramadan has lectured in France, England and the US, and also has had trouble with the US government.
He had his US visa revoked in 2004 shortly before he was to receive tenure at Notre Dame University in Indiana.
He was denied entry to the US in 2006 on the grounds that he had given $1,336 to a charity linked to Hamas, which the US considers a terrorist organisation.