The Northern Shoveler was first formally described by the Swedish naturalist Carl Linnaeus in 1758 in the tenth edition of his Systema Naturae. He introduced the binomial name Anas clypeata. A molecular phylogentic study comparing mitochondrial DNA sequences published in 2009 found that the genus Anas, as then defined, was non-monophyletic. The genus was subsequently split into four monophyletic genera with ten species including the northern shoveler moved into the resurrected genus Spatula. This genus had been originally proposed by the German zoologist Friedrich Boie in 1822. The name Spatula is the Latin for a "spoon" or "spatula". The specific epithet is derived from Latin clypeata, "shield-bearing" (from clypeus, “shield").
No living subspecies are accepted today. Fossil bones of a very similar duck have been found in Early Pleistocene deposits at Dursunlu, Turkey. It is unresolved, however, how these birds were related to the northern shoveler of today; i.e., whether the differences noted were due to being a related species or paleosubspecies, or attributable to individual variation.