Labeo worthingtoni was originally called Labeo intermedius by Worthington (1933), but this name was preoccupied and Henry W. Fowler provided it with its current name as a replacement in 1958. It was considered "[a] species of doubtful validity" by Jackson (1961). However, in his revision of Labeo, Reid (1985) recognized L. worthingtoni as a valid species endemic to Lake Malawi.

Worthington (1933: 298) had this to say about differentiating this labeo from the other two species then known in the lake:

The three type-specimens and the long series of both L. mesops and L. cylindricus in Dr. Christy's collection show clearly that this is a distinct species. It can be distinguished immediately from L. mesops by the lips, which have papillae fused into many rows of small transverse plicae, and by the smaller eye; and from L. cylindricus by the much deeper strongly compressed body and the much narrower under-lip.

The above drawing is reproduced from Text-figure 3 of Worthington (1933).

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