Hossein Loghmanian is one of three reformist MPs sentenced to jail for insulting the conservative judiciary.
Mr Loghmanian was given 10 months in Tehran's notorious Evin prison.
More than 60 other MPs of the majority reformist movement have been summoned to court, but Mr Loghmananian is the first to be jailed.
During a heated debate, some deputies called on Iran's supreme leader, Ayatollah Ali Khamenei, to intervene and stop the arrest of MPs.
Some MPs said the jailing was a sort of coup and called for a referendum on whether the court should continue its work.
'It's illegal'
Majority spokesman Davud Soleimani affirmed that "all MPs are prepared to go to jail" with their colleague.
"It's illegal and threatens national security and the interests of the regime," he said.
The conservatives acted as the parliament's Speaker, Mehdi Karroubi, was on a trip to Saudi Arabia.
Some see the arrest as a reaction to a speech, termed provocative by the conservatives, delivered by President Khatami last Thursday at Tehran university.
Arrests fear
The president said that the conservatives were undermining reforms and taking revenge on the Iranian electorate, who started the reform movement by voting him into office.
From Riyadh, Mr Karroubi called on the MPs to stay calm.
The row over immunity for MPs speaking in parliament or during political meetings, which the courts refuse to recognise, reflects the ongoing rivalry between conservative and reformist factions in Islamic Iran.
Our correspondent says that if the conservatives succeed in keeping Loghmanian in jail, more arrests are bound to follow soon, despite the protests of MPs and despite the fact that the Iranian constitution states that MPs should be completely free to express themselves.