"captain or master of a ship," late 14c., from Middle Dutch scipper, from scip (see ship (n.)). Compare English shipper, used from late 15c. to 17c. in sense "skipper." Transferred sense of "captain of a sporting team" is from 1830.
"one who skips," mid-15c., agent noun from skip (v.). As a type of butterfly, 1817, from its manner of flight.