History of "natural transformations"

Natural transformations were first introduced by Eilenberg and MacLane in the context of group theory, in Natural isomorphisms in group theory (1942) -- three years before their definition in the context of functors or categories.

_{Indeed, "three years before" is not "long before", but in the development of a concept it is a significant delay.}

See Whitney's paper from 1935 where he defined tensor products of abelian groups. There you will find the terms natural homomorphism and (especially) natural isomorphism. Whitney makes no attempt to give absolutely rigorous definitions of those concepts, as the motivation to do so was lacking, but his sense of "naturality" is what Eilenberg and Mac Lane were making precise in their introduction of natural transformations.

The words "natural homomorphism" and "natural isomorphism" are also used (mainly in the context related to the First Isomorphism Theorem) in Pontryagin's "Topological groups" (Russian edition 1938, English translation 1939). Google books confirms my memory of this here.