Berlinger was born to a Jewish family and graduated from Colgate University in 1983.

The first film Berlinger directed was the documentary Brother's Keeper (1992), which tells the story of Delbart Ward, an elderly man in Munnsville, New York, who was charged with second-degree murder following the death of his brother william. Film critic Roger Ebert called it "an extraordinary documentary about what happened next, as a town banded together to stop what folks saw as a miscarriage of justice."

Berlinger has also worked on TV series such as Homicide: Life on the Street, in 1999 D.C., in 2000 and FanClub in 2001.

Although Berlinger primarily is known for documentaries, he has made a number of films, such as Book of Shadows: Blair Witch 2 (2000).

In collaboration with Journalist Greg Milner, Berlinger has also written a book called Metallica: This Monster Lives (2004), which is about his journey in the documentary field through his time making Blair Witch 2 and up through directing and producing Some Kind of Monster (2004) with Metallica, the metal band.

Chevron Corporation subpoenaed the outtakes from Berlinger's 2009 film Crude. Berlinger fought the request, citing reporters' privilege, but in 2010 a federal judge ordered Berlinger to turn over more than 600 hours of footage created during the film's production. Berlinger appealed, but in 2011 the US 2nd Circuit Court of Appeals upheld the lower court ruling against Berlinger, though with a slight reduction in the total hours of footage required.

After a 2010 decision by the Arkansas Supreme Court regarding newly produced DNA evidence, attorneys for the West Memphis Three negotiated with prosecutors an Alford plea allowing them to assert their innocence while acknowledging enough evidence to convict them; the result, on August 19, 2011, was acceptance of the pleas by Judge David Laser, and his reduction of sentence of the three to time served, and their release with 10-year suspended sentences (after 18 years, 78 days in prison).

Berlinger is best known for the film series Paradise Lost, which documents the murder trial and the subsequent legal battles of three Arkansas teenagers, Damien Echols, Jason Baldwin and Jessie Misskelley Jr., wrongfully convicted of murder. The court convicted the youths (known as the West Memphis Three) of murdering three eight-year-old boys as part of a "ritual killing," although no physical evidence linked the three young men to the crime. Paradise Lost documents the 20-year ordeal of these three young men from arrest to conviction, through years of unsuccessful legal efforts, to a final successful appeal that resulted in their release in the summer of 2012.

As of February 2014, Berlinger was committed to the production of The System, an 8-part series on the American Criminal justice system, for Al Jazeera America.