Origin unknown. (Irish naigín, Scottish Gaelic noigean are both from English.) Compare nog. As a drink measure, perhaps related to naggin.
noggin (plural noggins)
- A small mug, cup or ladle.
- (dated) A measure equivalent to a gill.
- 1836, Charles Dickens, The Pickwick Papers
- I don’t know whether...you...ever...went out to a slight lunch of a bushel of oysters, a dozen or so of bottled ale, and a noggin or two of whiskey to close up with.
- (slang) The head.
- 2003, James D. Doss, Dead Soul 
- Or maybe he bumped his noggin when he fell down—after he got clipped on the legs.
- 2003, John Farris, The Fury and the Power 
- She bumped her noggin on the bulkhead above the doorway, smiled in apology for her presumed clumsiness.
- (biochemistry) A signalling molecule involved in embryo development, producing large heads at high concentrations.
- (New Zealand) Alternative form of nogging (“horizontal beam”)
measure equivalent to a gill