Besides unwillingly lending his name and reputation to a popular fictional character, Baron Munchausen's name has been applied to several scientific phenomena as well. Munchausen Syndrome is a psychological disorder in which sufferers lie about their health, inventing symptoms and ills to gain sympathy and attention. It was so-called by Dr. Richard Asher in 1951, who drew a comparison between the dramatic tall-tales told by the Baron and those relayed by patients.

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In more recent times, Munchausen syndrome has been noted to have some interesting variations. In Munchausen syndrome-by-proxy, it is a caretaker who fabricates an illness in a dependant. This is most often perpetrated on young children, often by falsifying test results, feigning symptoms, and sometimes even deliberate poisoning. An even newer adaptation of the disorder is Munchausen by Internet, where a person fakes having an illness online, usually on messageboards and social media. The term does not apply, however, when someone fakes an illness as part of a scam to make money, but only when the attention is the primary goal.

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Another usage for the name comes to us from philosophical circles, where the Munchausen trilemma is describes an important philosophical problem. Described by Hans Albert in the 1960's, the trilemma points out the inherent flaw in reaching a logical conclusion from a predefined premise. Because the premise is itself derived from some previous premise, and that one from still another, the truth can never be truly arrived upon, without falling into circular logic or belief. This phenomena is named after the incident where Baron Munchausen saves himself from drowning by pulling on his own hair, much like the saying "pulling yourself up by your own bootstraps."