pre-1600, from flap (v.) + jack (n.), using the personal name in its "generic object" sense. So called from the process of baking it by flipping and catching it in the griddle when done on one side.
Entries linking to flapjack
flap v.
early 14c., "dash about, shake, beat (the wings);" later "strike, hit" (mid-14c.); probably ultimately imitative. Meaning "to swing about loosely" is from 1520s. Related: Flapped; flapping.
jack n.
late 14c., jakke "a mechanical device," from the masc. name Jack. The proper name was used in Middle English for "any common fellow," and thereafter extended to various appliances which do the work of common servants (1570s). Also used generically of male animals (1620s, see jackass, jackdaw, etc.).
As a portable contrivance for raising weight by force from below, 1703. As the name of a device for pulling off boots from 1670s. The jack in a pack of playing cards (1670s) is in German Bauer "peasant." Slang meaning "money" is by 1890 (in earlier slang it meant "a small coin"). Jack-towel, one sewn together at the ends round a roller, is from 1795. The jack of Union Jack is a nautical term for "small flag at the bow of a ship" (1630s) and perhaps is from the word's secondary sense of "smaller than normal size."