Born John Parnell Thomas in Jersey City, New Jersey, after graduating from high school, he studied at the University of Pennsylvania. When the United States joined World War I in 1917, he served overseas with the United States Army. Following his discharge from the military in 1919, Thomas worked in the investment securities and insurance business in New York City for the next eighteen years.

J. Parnell Thomas entered Allendale, New Jersey municipal politics in 1925 and was elected to council then mayor between from 1926 to 1930. He was elected to a two-year term to the New Jersey General Assembly in 1935 and in 1936 was elected to the United States House of Representatives as a Republican Party Representative from New Jersey. He would be reelected six times.

As a U.S. Congressman, Thomas was a staunch right-wing opponent of President Franklin Delano Roosevelt and his "New Deal" claiming the President's legislative agenda had "sabotaged the capitalist system." Thomas opposed government support for the Federal Theatre Project declaring that: "Practically every play presented under the auspices of the Project is sheer propaganda for Communism or the New Deal." Unrelenting, in 1949 Thomas called the U.S. Secretary of Defence, James Forrestal, "the most dangerous man in America" and claimed that if he was not removed from office he would "cause another world war".

Following the Republican Party gaining control of the 80th Congress, J. Parnell Thomas was appointed chairman of the House Committee on Un-American Activities (HUAC). In May 1947, Thomas traveled to Hollywood to meet with film industry executives with a view to exposing what he believed was communist infiltration of motion pictures content by members of the Screen Writers Guild. Returning to Washington, he shifted the focus of the committee to what he called the "subversives" working in the film business. Under Thomas, in October of 1947, HUAC summoned suspected communists to appear for questioning. These summonses led to the conviction and imprisonment for contempt of Congress of the "Hollywood Ten" who had refused to answer the Committee's questions, citing the First Amendment.

Prominent American columnists Jack Anderson and Drew Pearson were critical of Thomas and his committee's methods. Rumors about corrupt practices on the part of Thomas were confirmed when his secretary, Helen Campbell, sent documents to Drew Pearson which he used to expose Thomas's corruption in an August 4, 1948 newspaper article. As a result, J. Parnell Thomas was summoned to answer to charges before a grand jury. In a twist of irony, Thomas refused to answer questions, citing First Amendment rights, the same as the Hollywood Ten had cited but which Thomas had refused to accept. Indicted, Thomas was tried and convicted of fraud and given a fine and an eighteen month prison sentence. He resigned from Congress on January 2, 1950. In one more twist of irony, he was imprisoned in Danbury Prison with Lester Cole and Ring Lardner, Jr. - both members of the "Hollywood Ten" serving time because of Thomas.

After his release from prison, J. Parnell Thomas returned to the practice of law and was also an editor and publisher of three weekly newspapers in Bergen County, New Jersey. President Truman pardoned him on Christmas Eve, 1952. In 1954, he tried to re-enter Federal politics but was defeated for the Republican party nomination for Congress.