late 14c., rectour (late 13c. as a surname, early 13c. in Anglo-Latin), "ruler of a country or people" (a sense now obsolete), from Latin rector "ruler, governor, director, guide," from rect-, past participle stem of regere "to rule, guide" (from PIE root *reg- "move in a straight line," with derivatives meaning "to direct in a straight line," thus "to lead, rule").
The meaning "head of a college or religious community" is by early 15c., though the exact religious sense varies across place and time and with different denominations. Used originally of Roman governors and God; by 18c. generally restricted to clergymen and college heads. Fem. forms were rectress (c. 1600); rectrix (1610s). Related: Rectorship; rectorial.