In this paper, we show how to construct exceptional orthogonal polynomials (XOP) using isospectral deformations of classical orthogonal polynomials. The construction is based on confluent Darboux transformations, where repeated factorizations at the same eigenvalue are allowed. These factorizations allow us to construct Sturm–Liouville problems with polynomial eigenfunctions that have an arbitrary number of real‐valued parameters. We illustrate this new construction by exhibiting the class of deformed Gegenbauer polynomials, which are XOP families that are isospectral deformations of classical Gegenbauer polynomials.