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.)).

The word secretary is related to secret. It comes from the medieval Latin secretarius, which could mean a sanctuary or hiding place, a person in charge of a church’s vestments, or a confidential advisor or agent.