1550s, originally an ecclesiastical word meaning "bishop" or "minister who supervises churches within a district" (ultimately a loan-translation of Greek episkopos "overseer"), from Medieval Latin superintendentem (nominative superintendens), present participle of Late Latin superintendere "oversee," from Latin super "above" (see super-) + intendere "turn one's attention to, direct" (see intend). Famously used by 16c. radical Protestants in place of bishop, which to them was tainted by Papacy.
[Martinists] studie to pull downe Bishopps, and set vp Superintendents, which is nothing else, but to raze out good Greeke, & enterline bad Latine. [Lyly, "Pappe with an Hatchet," 1589]
The general sense of "a person who has charge of some business" is first recorded 1580s. Meaning "janitor, custodian" is from c. 1935. Shortened form super first attested 1857, especially at first of overseers of sheep ranches in Australia. As an adjective meaning "superintending," from 1590s.