We develop a numerical linked cluster expansion (NLCE) method that can be applied directly to inhomogeneous systems, for example Hamiltonians with disorder and dynamics initiated from inhomogeneous initial states. We demonstrate the method by calculating dynamics for single-spin expectations and spin correlations in two-dimensional spin models on a square lattice, starting from a checkerboard state. We show that NLCE can give moderate to dramatic improvement over an exact diagonalization of comparable computational cost, and that the advantage in computational resources grows exponentially as the size of the clusters included grows. Although the method applies to any type of NLCE, our explicit benchmarks use the rectangle expansion. Besides showing the capability to treat inhomogeneous systems, these benchmarks demonstrate the rectangle expansions utility out of equilibrium.