Apel worked in ethics, the philosophy of language and human sciences. He wrote extensively in these fields, publishing mostly in German. Apel's work brings together the Analytical and Continental philosophical traditions, especially pragmatism and the critical theory of the Frankfurt School.

In Understanding and Explanation: A Transcendental-Pragmatic Perspective,^[5] Apel reformulated the difference between understanding (Verstehen) and explanation (Erklärung), which originated in the hermeneutics of Wilhelm Dilthey and interpretive sociology of Max Weber, on the basis of a Peircean-inspired transcendental-pragmatic account of language. This account of the "lifeworld" would become an element of the theory of communicative action^[6]and discourse ethics, which Apel co-developed with Jürgen Habermas. Strategic rationality both claim to stand in need of communicative rationality that is seen as, in several regards, more fundamental.^[7] While sympathetic to Habermas's Theory of Communicative Action, Apel has been critical of aspects of Habermas's approach. Apel has proposed that a theory of communication should be grounded in the transcendental-pragmatic conditions of communication. After taking his point of departure from Apel, Habermas has moved towards a "weak transcendentalism" that is more closely tied to empirical social inquiry.

Apel has also written works on Charles Sanders Peirce and is a past president of the C.S. Peirce Society.

An early German-speaking adversary of so-called critical rationalism, Apel published a critique of the philosophy of Karl Raimund Popper: InTransformation der Philosophie (1973), Apel charged Popper with being guilty of, amongst other things, a pragmatic contradiction.^[8][9]

From the 1970s to the 1990s, Apel influenced some other philosophers writing in Europe, the Americas, and Asia.