He is a paranormal investigator of unidentified flying objects, having researched many sightings and written critiques of the hypothesis that UFOs are alien spacecraft.

He was a founding member (with Philip J. Klass and James Oberg) of the UFO Subcommittee of the Committee for Skeptical Inquiry, and is a former fellow of that organization.

They will typically grab onto any photo or video that is supposed to represent the object and report as fact practically any claim that is made regardless of its source or veracity."

As Sheaffer summarizes it on his blog, "A bright, glowing orange UFO is allegedly seen over the base by security men, and then the Oscar Flight missiles were said to start going off-line, one by one.

"[9] As for the base's missiles going off-line, Sheaffer could find no evidence or paper trail to support that, only the claim of (then) Air Force Lieutenant Robert Salas.

Noted UFO researcher Robert Hastings responded to Sheaffer's investigation by dismissing the possibility that the glowing object was Mars.

Former SAC missile crew commander Tim Hebert goes further than Sheaffer, stating on his blog "At this point in time there is no supporting documentation or statements from security personnel corroborating the claims for what, if anything, was observed out in the field.

"[10] Called "one of the—if not the—world's top experts on the subject of unidentified flying objects and claims of extraterrestrials" by paranormal investigator Ben Radford in a review of Sheaffer's book Bad UFOs: Critical Thinking About UFO Claims, Radford states that Sheaffer has "encyclopedic knowledge of a surprisingly diverse topic" and uses it in the book.

[12] Sheaffer rejects the science of global climate change, writing in 2008 that, "when a prominent theory is opposed by scientists of the caliber of Richard Lindzen of MIT, Reid Bryson of the University of Wisconsin, Freeman Dyson of the Institute for Advanced Study, and many others, it is disingenuous to speak of a 'consensus.'"

[15] On his debunker blog, Sheaffer calls modern (post-1960s) feminism a con, and compares it to astrology and parapsychology in its lack of academic peer review, poor scholarship, and prevalence of false and inaccurate information and claims.

'"[18] In his 1991 book The Making of the Messiah, Sheaffer argues that Christianity developed "from the envious anger of the lower classes" towards "Roman power and wealth.

[19] Sheaffer writes that Christ's claim to operate under a "higher law" came from his resentment at being "despised and rejected" in Jewish society due to the circumstances of his birth.

"[19] The twentieth episode of the third season of the X-Files television series, entitled "Jose Chung's From Outer Space", referenced Robert Sheaffer.

The plot featured US Air Force test pilots, dressed as aliens, who flew a secret military aircraft designed to resemble a UFO.

[27] He spoke at the "Animal Mutilations, Star Maps, UFOs and Television" session of the "Science, Skepticism and the Paranormal" conference put on by CSICOP in 1983.

[32][33] Sheaffer is a member of Mensa International, having been introduced to it by Robert Steiner (1934–2013, fellow of the Committee for Skeptical Inquiry, president of the Society of American Magicians from 1988 to 1989).