Isikoff received his A.B. from Washington University in 1974, and obtained a masters from the Medill School of Journalism from Northwestern University in 1976. He graduated from Syosset High School on Long Island in 1970. Isikoff is the co-author, with The Nation reporter David Corn, of Hubris: The Inside Story of Spin, Scandal and the Selling of the Iraq War, a 2006 book about the selling of the 2003 Invasion of Iraq to the US public and the ensuing Plame scandal. The book was a New York Times best-seller.

His online column with fellow journalist Mark Hosenball, “Terror Watch,” won the 2005 award from the Society of Professional Journalists for best investigative reporting online. Isikoff was a part of the Newsweek team that won the Overseas Press Club’s most prestigious award, the 2001 Ed Cunningham Memorial Award for best magazine reporting from abroad for Newsweek’s coverage of the war on terror.

In the May 9, 2005 issue of Newsweek, Isikoff wrote an article that stated that interrogators at Guantanamo Bay "in an attempt to rattle suspects, flushed a Qur'an down a toilet." Detainees had earlier made similar complaints but this was the first time a government source had appeared to confirm the story. The article caused widespread rioting and massive anti-American protests throughout some parts of the Islamic world (causing at least 17 deaths in Afghanistan). The magazine later retracted the story after noting that the anonymous official who was their source subsequently could not remember important details.

Isikoff has been a contributing blogger at The Huffington Post.

Several writers have raised questions about Mr. Isikoff's objectivity, specifically citing concerns that some of his stories are slanted to portray matters in a more favorable light where some high-powered officials are concerned. More recently FBI whistleblower Sibel Edmonds has accused Isikoff of deliberately covering up potentially explosive revelations and corroborating evidence she provided him when he reported her story for Newsweek. Her evidence included among other things a Justice Department Inspector General's Report and statements from members of Congress supporting allegations of "security breaches, possible espionage incidents, and severe mismanagement involving the FBI Translation Division". Significantly one of the Inspector General's Reports concluded "[s]ome of the most serious weaknesses still have not been fully remedied and expose the FBI to the risk of serious compromises by other moles" (note the word "other"). Mr. Isikoff was also given the names of other FBI whistleblowers willing to corroborate, some of whom wanted to remain anonymous. Yet in Mr. Isikoff's reporting he made use of none of this, simply repeating the FBI's previously discredited excuse that all the problems were due to a "shortage" of translators. Before publishing an account of the incident on her blog Ms. Edmonds contacted Mr. Isikoff for a response to her story. He replied simply "Sibel- Sorry. No comment. Regards, Mike".