Marr attended Sydney Church of England Grammar School in North Sydney and subsequently graduated from the University of Sydney with degrees in Arts and Law. Marr worked for a time as an articled clerk at the law firm Allen, Allen and Hemsley, before turning to journalism.

Marr began as a journalist working for The Bulletin magazine and for The National Times newspaper, before being appointed editor in 1981—82. During this period, he oversaw the publication of the articles by David Hickie that detailed long-suppressed allegations of corruption against former New South Wales Premier Robert Askin. The first article, headlined "Askin: friend of organised crime" was famously published on the day of Askin's funeral in 1981.

Marr was a reporter on the ABC TV program Four Corners (1985, 1990—91), a role in which he won a Walkley Award, and presenter of Radio National's Arts Today program (1994—96). From 2002 to 2004, he hosted the ABC TV program Media Watch. He currently works for The Sydney Morning Herald. He is a frequent guest on ABC TV's Insiders program. During his term as presenter of Media Watch, he played a key role in exposing the ongoing cash for comment affair, which Media Watch had first raised in 1999, concerning radio commentators Alan Jones and John Laws. In 2004, the program's exposé of Australian Broadcasting Authority (ABA) head David Flint — who had written fan letters to Jones at a time when Jones was being investigated by the ABA — played a significant role in forcing Flint's resignation.

In 2002, Marr demonstrated on Media Watch that conservative newspaper columnist Janet Albrechtsen had misquoted a French psychiatrist, Jean-Jacques Rassial, and claimed that she had done this deliberately to make it look as though violence and gang rape were institutionalised elements of the culture of Muslim youths.Albrechtsen did not deny the misquote, but responded by accusing Media Watch of inherent left-wing bias, and of deliberately leading a witch-hunt against contrary views. When the Minister for Communications, Senator Helen Coonan, appointed Albrechtsen to the board of the ABC in February 2005, Marr publicly questioned whether she was qualified for such a position in light of her prior breach of journalistic conduct.

Marr has published several books including a critically acclaimed biography of Australian writer Patrick White, which won The Age Book of the Year award and the New South Wales Premier's Literary Award for Non-Fiction. More recently, Marr wrote, along with Marian Wilkinson, Dark Victory, an account of the 2001 Australian election campaign in the wake of the Tampa affair.

His books include:

• Barwick 1980
• The Ivanov Trail 1984
• A Life 1991
• Letters 1994
• The High Price of Heaven 2000
• Dark Victory (with Marian Wilkinson) 2004 ISBN 0-14-300258-9
• Quarterly Essay Issue 26, His Master’s Voice: The Corruption of Public Debate under Howard 2007 ISBN 978-1-86395-405-1
• The Henson Case 2008 ISBN 978-1-92152-003-7
• The Political Journey of Kevin Rudd, 2010