The term was first documented in the early "Mercury" days of the US space program. It came there from a Yale graduate named John Rawlings who helped design the astronauts' space suits. The phrase is actually derived from an earlier, more vulgar and direct term which was slang for doing something very much the wrong way, as in "you are **** the dog!" At Yale a friend of Rawlings', the radio DJ Jack May (a.k.a. "Candied Yam Jackson") amended this term to "screwing the pooch" which was simultaneously less vulgar and more pleasing to the ear.

The term, however, did not enter the popular lexicon until Tom Wolfe used it in his book about the space program, The Right Stuff, where it was used to describe a supposed mistake by astronaut Gus Grissom.

The phrase's origins come from an old joke. There are various versions, but a drunk man ends up shooting the wife and screwing the pooch (instead of the other way around).