late 14c., secretarie, "person entrusted with secrets or private and confidential matters" (a sense now obsolete), from Medieval Latin secretarius "clerk, notary, scribe; confidential officer, confidant," a title applied to various confidential officers, noun use of an adjective meaning "private, secret, pertaining to private or secret matters" (compare Late Latin secretarium "a council-chamber, conclave, consistory"), from Latin secretum "a secret, a hidden thing" (see secret (n.)).
Compare Late Latin silentiarius "privy councilor, 'silentiary,' " from Latin silentium "a being silent." The specific meaning "person who keeps records or minutes, conducts correspondence, etc., one whose office is to write for another," originally for a king, is recorded by c. 1400. As title of ministers presiding over executive departments of state, it is from 1590s. The word also is used in both French and English to mean "a private desk," sometimes in French form secretaire.
As a type of handwriting used on old legal documents, 1570s. The carnivorous South African secretary bird is said to be so called (1786) in reference to its crest, which, when smooth, resembles a pen stuck over the ear.