In the milestoning framework, and more generally in related transition interface sampling schemes, one significantly enhances the calculation of relaxation rates for complex equilibrium kinetics from molecular dynamics simulations between the milestones or interfaces. The goal of the present paper is to advance milestoning applications into the realm of non-equilibrium statistical mechanics, in particular, to calculate entire time correlation functions. In order to accomplish this, we introduce a novel methodology for obtaining the flux through a given milestone configuration as a function of both time and initial configuration and build upon it with a novel formalism describing autocorrelation for Langevin motion in a discrete configuration space. The method is then applied to three different test systems: a harmonic oscillator, which we solve analytically, a two-well potential, which is solved numerically, and an atomistic molecular dynamics simulation of alanine dipeptide.