After serving three years as a navigator and intelligence officer in the Strategic Air Command, Franklin got his doctorate at Stanford University and then became an associate professor of English there. He was a prominent activist in the movement against the Vietnam War. In the late 1960s, he was one of the founders of the Revolutionary Union, a Maoist organization, but in 1971 he split, along with about half the membership of the RU, to join the revolutionary Venceremos Organization. Venceremos and Franklin were specifically targeted by the FBI COINTELPRO effort. Franklin's political views and actions during that period were public, and continued despite being targeted by the FBI's COINTELPRO, which used disinformation, agents provocateurs, and violent acts to discredit leftist organizations. Documents obtained under the Freedom of Information Act show many attempts by the FBI to "neutralize" Franklin.

Stanford fired Franklin, even though he had academic tenure, for leading a group of students to occupy the computer center in 1972 and urging students and faculty to strike in protest against the invasion of Laos and Stanford's involvement in the war. Firing a tenured professor was quite a feat: the University's rules provided for due process. A tenure-review committee was chosen, from professors outside Franklin's department, composed of associate or full professors who had hopes of advancement: two of them expected to become President of Stanford some day, and one of them actually did...Donald Kennedy. A medium-sized Physics lecture hall was converted into a courtroom with the usual furniture and paraphernalia. A Los Angeles attorney, Paul Valentine, was retained to plead the University's case. Franklin defended himself, with advice from a law student and a well-known constitutional lawyer. Evidence was heard for each side, witnesses were cross-examined, and summations given, and the panel left the room to consider its verdict, which was guilty of violating the university's Disruption Policy, punishable by revocation of tenure and termination with prejudice.

Franklin was blacklisted and without regular employment for three years (although he had brief visiting faculty positions at Wesleyan University and Yale). In 1975 he was hired as a (tenured) full professor at Rutgers, where he has since been named the John Cotton Dana Professor of English and American Studies, and has received numerous awards for teaching and scholarship.

Franklin is the author or editor of nineteen books and hundreds of articles on culture and history published in more than a hundred different academic journals, major magazines and newspapers, reference works, and anthologies. He has given over five hundred addresses on college campuses, on radio and TV shows, and at academic conferences, museums, and libraries; he has participated in the making of four films.

Franklin’s main subject is American history and culture; his work aims at interdisciplinarity and broad public accessibility. He started out as a scholar of Herman Melville; his first book, The Wake of the Gods: Melville’s Mythology, which has been in print since its publication in 1963, examines Melville's use of mythologies most 20th-Century scholars are not familiar with: one expects references to Judaeo-Christian or Greco-Roman lore, but Melville's intellectual milieu was well-informed on many other cultures, from Meso-American to Sanskrit. In addition, Franklin produced a scholarly edition of Melville's The Confidence Man: His Masquerade, which traces many obscure classical and "alien" references embedded in Melville's prose. This has recently been reprinted, but its numerous and tendentious footnotes may annoy readers who prefer to experience Melville in his own words.

His second book, Future Perfect: American Science Fiction of the Nineteenth Century (1966), which has gone through several editions and been widely adopted as a classroom text, inaugurated the serious study of science fiction and identified such classic American authors as Irving, Poe, Hawthorne, and Melville as pioneers of this genre, hitherto largely neglected by literary critics. His Robert A. Heinlein: America as Science Fiction won awards in 1981 and 1983; in 1990 he was named the Distinguished Scholar for the International Association for the Fantastic in the Arts. In 1991 he was Guest Curator for the “Star Trek and the Sixties” exhibit at the National Air and Space Museum of the Smithsonian Institution; this show subsequently traveled to the Hayden Planetarium.

Prison Literature in America: The Victim as Criminal and Artist established Franklin as a leading authority on American prison literature. Released in 1989 into an expanded third edition, this book has been widely used by historians, penologists, literary critics, and sociologists. Franklin’s 1998 anthology Prison Writing in 20th-Century America is a basic classroom text.

In his 1988 War Stars: The Superweapon and the American Imagination, Franklin turned his interest in science fiction to an examination of the American fascination with superweapons. His book presents a view that, ironically, from Robert Fulton’s submarine Nautilus in the eighteenth century to the death-dealing weaponry of the late twentieth century, superweapons ostensibly designed to end war have proved capable of exterminating the human species. War Stars is informed by Franklin’s own earlier experience as a former navigator and intelligence officer in the Strategic Air Command.

Franklin has been publishing on the history of the Vietnam War and its role in American literature and culture since 1966. His M.I.A., or Mythmaking in America, and his co-edited Vietnam and America: A Documented History have been widely used in courses on the Vietnam War. His 2000 book Vietnam and Other American Fantasies synthesizes this previous work and extends it into an overview of 21st-century American culture. One of Franklin's major themes in writing about Vietnam is that the supposed existence of surviving U.S. prisoners of war in Vietnam after the war is a myth created after 1980 with the aid or tacit approval of the Reagan White House, and that the psychological foundation of the myth arguably lies in the justifications the Nixon White House offered for the Vietnam War in the years before 1973: namely, that it was a war to bring the POWs home.

Franklin’s most recent book, The Most Important Fish in the Sea: Menhaden and America (2007), is an interdisciplinary study of the role of menhaden in American environmental, economic, social, political, and cultural history from the seventeenth into the twenty-first centuries.