This rhyme was probably written by Thomas Muffet, a doctor and an entomologist who lived during the late sixteenth century. Thomas Muffet fancied himself to be quite a poet, and even composed a poem on silkworms! Little Miss Muffet is supposed to be his daughter, Patience.

Some scholars suggest that the rhyme could have been associated with the Cushion Dance. This was a dance popular in England during the 16th century. The dance was associated with mating and marriage rituals and the May Day festival. The dance would begin with a single person, man or woman, dancing round the room with a cushion (the tuffet). When the music stopped, the dancer, if he were a man, would lay the cushion before a woman (and if a woman, then before a man), and invite the second person to join in. The second person would kneel on the cushion and the first dancer would kiss her (or him) and then both would continue the dance. When the music stopped again, it would be the turn of the second dancer to invite a third person to join in. And so the dance would carry on.

Another theory is that the rhyme refers to Mary, Queen of Scots, who was supposed to have been frightened by John Knox, a Scottish clergyman and religious reformer. But this seems unlikely.

The rhyme does not seem to have been printed before 1805.