Philipse has written many philosophical works in Dutch, including books on Husserl's early philosophy of logic, the role of certainty in Descartes' moral theory, and a widely read Atheist Manifesto (1995, 2004).

He has also written many commentaries for Dutch newspapers (most frequently as a regular contributor to the NRC Handelsblad) and current events television programs, defending atheism and advocating cultural assimilation for non-European immigrants in the Netherlands.

In his philosophical work, Philipse defends a non-reductionist naturalism, akin to that of Gilbert Ryle, Peter Strawson, and P.M.S.

While highly critical of the transcendental idealist tradition of Kant and Husserl for its allegedly incoherent notion of conceptual schemes, Philipse argues that scientistic philosophies that attempt to reduce consciousness to purely physical descriptions (such as those of Quine and Churchland) fall victim to a similar inconsistency: their theories logically depend on the concepts of ordinary human life they would abolish.

More generally, Philipse firmly defends the values of the Enlightenment: support for the natural sciences and political liberalism.