late 14c., "arithmetical symbol for zero," from Old French cifre "nought, zero," Medieval Latin cifra, with Spanish and Italian cifra, ultimately from Arabic sifr "zero," literally "empty, nothing," from safara "to be empty;" loan-translation of Sanskrit sunya-s "empty." The word came to Europe with Arabic numerals. Originally in English "zero," then "any numeral" (early 15c.), then (first in French and Italian) "secret way of writing; coded message" (a sense first attested in English 1520s), because early codes often substituted numbers for letters. Klein says Modern French chiffre is from Italian cifra.

"to do arithmetic" (with Arabic numerals), 1520s, from cipher, n.. Meaning "to write in code" is from 1560s. Related: Ciphered; ciphering.