mid-14c., "imported oak of superior quality" (well-grained and without knots), probably from Middle Dutch or Middle Flemish waghenscote "superior quality oak wood, board used for paneling" (though neither of these is attested as early as the English word), related to Middle Low German wagenschot (late 14c.), from waghen (see wagon) + scote "partition, crossbar" (from PIE root *skeud- "to shoot, chase, throw").
So called perhaps because the wood originally was used for wagon building and coachwork, but the sense evolution is not entirely clear. Meaning "panels lining the walls of rooms" is recorded from 1540s. Wainscoting is from 1570s.