During World War II, Hynek was a civilian scientist at the Johns Hopkins Applied Physics Laboratory, where he helped to develop the United States Navy's radio proximity fuze.

A special camera was devised for the task and a prototype was built and tested and then stripped apart again when, on Oct. 4, 1957, the Soviet Union launched its first satellite, Sputnik 1.

In April 1953, Hynek wrote a report for the Journal of the Optical Society of America titled "Unusual Aerial Phenomena," which contained one of his best-known statements: Ridicule is not part of the scientific method, and people should not be taught that it is.

Or, if there isn't, does not an obligation exist to say so to the public—not in words of open ridicule but seriously, to keep faith with the trust the public places in science and scientists?

He once said, "As a scientist I must be mindful of the lessons of the past; all too often it has happened that matters of great value to science were overlooked because the new phenomenon did not fit the accepted scientific outlook of the time.

He didn't do two things that some of them did: give you the answer before he knew the question; or immediately begin to expound on his accomplishments in the field of science.

Hynek has also stated his opinion that after Ruppelt's departure, Project Blue Book was little more than a public relations exercise, further noting that little or no research was undertaken using the scientific method.

[10] It was during the late stages of Blue Book in the 1960s that Hynek began speaking openly about his disagreements and disappointments with the Air Force.

Among the cases about which he openly dissented with the Air Force were the highly publicized Portage County UFO chase, in which several police officers chased a UFO for half an hour, and the encounter of Lonnie Zamora, a police officer who reported an encounter with a metallic, egg-shaped aircraft near Socorro, New Mexico.

[11] In late March 1966 in Dexter, Michigan, two days of mass UFO sightings were reported, and received significant publicity.

But much to his chagrin, Hynek's qualifications of his hypothesis were largely overlooked, and the term swamp gas was repeated ad infinitum in relation to UFO reports.

In his reply dated October 7, 1968, to a request for scientific recommendations regarding Blue Book from Colonel Raymond Sleeper, commander of the USAF Foreign Technology Division, Hynek noted that Blue Book suffered from numerous procedural problems and a lack of resources, which rendered its efforts "totally inadequate".

In November 1978, Hynek presented a statement on UFOs before the United Nations General Assembly's Special Political Committee on behalf of himself, Jacques Vallée, and Claude Poher.

At the MUFON annual symposium in 1973, held in Akron, Ohio, Hynek first expressed his doubts regarding the extraterrestrial (formerly interplanetary or intergalactic) hypothesis, in a speech titled "The Embarrassment of the Riches".

Jacques Vallee's journal entry of August 2, 1967, recounts a conversation with Hynek over lunch that day during which, "We turned to the subject of hypotheses.

"[15] In a paper presented to the Joint Symposium of the American Institute of Aeronautics & Astronautics in Los Angeles in 1975, he wrote, "If you object, I ask you to explain—quantitatively, not qualitatively—the reported phenomena of materialization and dematerialization, of shape changes, of the noiseless hovering in the Earth's gravitational field, accelerations that—for an appreciable mass—require energy sources far beyond present capabilities—even theoretical capabilities, the well-known and often reported E-M (electro-magnetic interference) effect, the psychic effects on percipients, including purported telepathic communications.

"[19] In Jacques Vallee's Foreword to his 1992 collection of journal entries from 1957-1969, he writes that Hynek, looking far less than millions of years into the future, "liked to remind us that beyond today's science there would be a twenty-first century science that would have to take into account phenomena that seemed paranormal to us simply because of our parochial mental attitudes and the limitations of what he aptly called our cultural provincialism.

[25] At the end of the film, after the abducted World War II fighter pilots disembark from the "mother ship", he can be seen, bearded and with pipe in mouth, stepping forward to view the spectacle.

[26] In his book UFOs: The Public Deceived,[27] the chapter on "Eyewitness Unreliability" begins (p. 81) with criticism of Hynek's insistence "for many years that no useful insights could be gained from the study of UFO reports that proved to be IFOs" (i.e., subsequently identified), as Hynek reiterated to a congressional committee in 1968: "These have little scientific value ... ; it matters not whether 100 or 100,000 people fail to identify [for example] an artificial satellite or a high–altitude balloon.

"[28] Rather, argues Klass, "UFO reports that prove to be IFOs show that intelligent people, including pilots, scientists, and law–enforcement officers, unwittingly embellish their accounts with inaccurate details and seeming cause–effects that are really unrelated.

He quotes Hynek as telling the Spiritual Frontiers Fellowship, "I can feel freer [here] to discuss the more esoteric aspects of the subject of UFOs.

Thus, this decade of CUFOS effort has provided what Hynek in 1967 called evidence of 'great negative significance,' that is, that there is no mysterious UFO phenomenon" (emphasis in original).

'"[35] In UFO Sightings: The Evidence, Sheaffer further concludes that ufology, as practiced by Hynek (and others), is "a powerful social movement [that is] fundamentally a reaction against science and reason" (emphasis in original).

An excerpt: "While I think such an award is an excellent idea, I have chosen not to participate in the process because of your inclusion of Dr. Allen Hynek on your panel of judges.

[37] Researcher Curt Collins, in a comprehensive weblog titled "Dr. Hynek and the UFO Photo Investigation of 1967," chronicles Hynek's role as an "[unwitting] secondary dupe" in fanning the flames of what would become an indelible UFO–photo case—thanks in large part to the Associated Press and the CBS Evening News with Walter Cronkite—involving several Polaroid instant photographs of a "hamburger"–shaped object taken on January 9, 1967, by the two lone "witnesses," Michigan teenage brothers Dan and Grant Jaroslaw.

[38] Hynek was unfortunately denied the original prints by the family, and it would be nine years before a letter of confession from the brothers would ultimately convince him of their hoax.

'"[38] [Apparently unbeknownst to Hynek at the time—despite an article widely disseminated by the Associated Press nearly a week prior to his initial endorsements—a local newspaper reporter, being shown the original prints within hours of the incident and observing Polaroid's sequential serial numbers on the reverse sides, noted that the photographs' sequencing was incompatible with the brothers' chronology of events.

He notes that "Since his teens Hynek had been an enthusiastic though closeted student of the occult" with "a particular fondness for the writings of the Rosicrucian secret societies, with their tantalizing promises of hidden ancient knowledge, and those of the so–called hermetic philosophers, especially Rudolf Steiner," and "even endorsed alleged instances of 'psychic surgery' and 'psychic photography.'"

For these and other reasons, Franch asserts that Hynek's initial "skeptical attitude" toward UFO reality "was in fact a façade for public consumption.

[42][43] In 2019, The History Channel created and aired a highly-fictionalized TV show based on his UFO research and the organization he worked for dubbed Project Blue Book.