A non-stationary flow in a network of thin tubes is considered. Its one-dimensional approximation was proposed in a paper by G.Panasenko and K.Pileckas, Flows in a tube structure: equation on the graph, JMP (2014). It consists of a set of equations with weakly singular kernels, on a graph, for the macroscopic pressure. A new difference scheme for this problem is proposed. Several variants are discussed. Stability and convergence are carefully investigated, theoretically and numerically. In addition, numerical results are compared to the direct numerical solution of the full dimension Navier-Stokes equations.