Son of a Boston firefighter, Loftus is a graduate of Boston College (BA, 1971) and Suffolk University (JD, 1977).

He served in the [[United States Army|U.S. Army]] from 1971 to 1974, attaining the rank of First Lieutenant. He began working for the [[US Department of Justice]] in 1977 and in 1979 joined their [[U.S. DOJ Office of Special Investigations|Office of Special Investigations]], which was charged with prosecuting and deporting [[Nazism|Nazi]] war criminals in the US. Loftus' now-expired Web site claimed, "As a young U.S. Army officer, John Loftus helped train Israelis on a covert operation that turned the tide of battle in the 1973 Yom Kippur War."

John J. Loftus is the author and co-author of several controversial books on Nazis, espionage, and similar topics including The Belarus Secret (1982), Unholy Trinity: How the Vatican's Nazi Networks Betrayed Western Intelligence to the Soviets (1992), The Secret War Against the Jews: How Western Espionage Betrayed the Jewish People (1994), Unholy Trinity: The Vatican, the Nazis, and the Swiss Banks (1998). Although Loftus' first book, "The Belarus Secret," is nonfiction, it was adapted into a TV-film, The Belarus File (1985), with Telly Savalas reprising his role from his television series, Kojak.

America's Nazi Secret, published in autumn 2010, has this text on its dust jacket:

"Despite government censorship, the original version of this book was the Knopf Nominee for the Pulitzer Prize in History, and earned 60 Minutes an Emmy Award for Outstanding Investigative Journalism. Thirty years later, this final manuscript has not been submitted for government review. All the censored items, and more, much more, are revealed for the first time. A third of modern history has been classified, until now.

"The Nuremburg trials were fixed. The US Justice Department did it. Some of America's finest families had funded Hitler. Ambitious lawyers in Washington covered it up under a cloak of national security. The Justice Department brought Nazis into America by the thousands to be trained as cold war spies.

"The Attorney General personally sponsored some of the worst war criminals for immigration to the USA, including the chief of the Ukrainian security service, Mykola Lebed. His troops murdered tens of thousands of Poles, Ukrainians and Jews, including Simon Wiesenthal's mother.

"In 1985, the Justice Department pawned this Ukrainian mass murderer off to Congress as an innocent leader of the Anti-Nazi resistance. Almost everything the Justice Department has ever told Congress about Nazis in America has been a willful and deliberate lie. The hunt for Nazi war criminals has been a mere public relations event to placate the Jews and WWII veterans.

"It gets worse.

"For sixty years, Justice has remained the legal shield of the Arab Nazi network, known as the Muslim Brotherhood. America is the only major nation still refusing to designate the Brotherhood as a terrorist group. Thirty years ago Justice Department Attorney John Loftus read the Top Secret Files and was ordered into silence under threat of imprisonment. Now the declassification clock has run down. Loftus says it is time for Justice to face the jury about where the Arab Nazi connection went wrong and who is really to blame for 9/11."

Loftus has a radio show on the Talkline Communications Network that broadcasts live every Monday and Tuesday from 11 pm to midnight EST in New York City; northern New Jersey; southern Connecticut; Miami, Florida; and Pompano Beach, Florida.

Loftus' friend, John Batchelor, is a co-host on the radio show. Batchelor's first appearance on the Loftus Report was met with great enthusiasm.

Loftus serves as a media commentator, appearing regularly on ABC National Radio and Fox News.

On August 7, 2005, he provided the United States address of an alleged terrorist named Iyad K. Hilal on Fox News. Only afterwards was it revealed that Hilal had left the address three years previously and the home was now owned by a family, which was then subjected to threats and vandalism and required police protection as a result of Loftus' words. Fox fired Loftus after the event. Loftus said "I thought it might help police in that area now that we have positively identified a terrorist," but he did not say why he did not contact police in a more direct manner. Loftus apologized for the mistake and expressed frustration about FBI inaction on an earlier tip he had given them years ago due to the same address.

On November 5, 2007 Loftus was awarded the Distinguished Eagle Scout Award by the Boy Scouts of America.