We introduce and study a class of multivariate rational functions associated with hyperplane arrangements, called flag Hilbert-Poincaré series. These series are intimately connected with Igusa local zeta functions of products of linear polynomials, and their motivic and topological relatives. Our main results include a self-reciprocity result for central arrangements defined over fields of characteristic zero. We also prove combinatorial formulae for a specialization of the flag Hilbert-Poincaré series for irreducible Coxeter arrangements of types $\mathsf{A}$, $\mathsf{B}$, and $\mathsf{D}$ in terms of total partitions of the respective types. We show that a different specialization of the flag Hilbert-Poincaré series, which we call the coarse flag Hilbert-Poincaré series, exhibits intriguing nonnegativity features and - in the case of Coxeter arrangements - connections with Eulerian polynomials. For numerous classes and examples of hyperplane arrangements, we determine their (coarse) flag Hilbert-Poincaré series. Some computations were aided by a SageMath package we developed.