"man ordained in the ministry," c.1200, from Old English cleric and Old French clerc "clergyman, priest; scholar, student," both from Church Latin clericus "a priest," noun use of adjective meaning "priestly, belonging to the clerus" (see cleric).
Modern bureaucratic usage is a reminder of the dark ages when clergy alone could read and write and were employed for that skill by secular authorities. In late Old English the word can mean "king's scribe; keeper of accounts;" by c.1200 clerk took on a secondary sense in Middle English (as the cognate word did in Old French) of "anyone who can read or write." This led to the sense "assistant in a business" (c.1500), originally a keeper of accounts, later, especially in American English, "a retail salesman" (1790). Related: Clerkship.