Abstract This work is focussed on the development of a numerical simulation model that predicts the thermal and fluid-dynamic behaviour of the two-phase flow distribution in systems with multiple branching tubes like manifolds. The geometry of a simulated branching system is represented as a set of tubes connected together by means of junctions. On one side, the in-tube evaporation/condensation phenomena are simulated by means of a one-dimensional two-phase flow model, and on the other side, the splitting/converging flow phenomena occurring at junctions are predicted with appropriate junction models obtained from the technical literature. The global flow distribution is calculated using a semi-implicit pressure based method (SIMPLE-like algorithm) where the continuity and momentum equations of the whole domain are solved and linked with both the in-tube two-phase flow model and the junction models. In the present paper, the flow distribution model is described and its most significant aspects are detailed. Furthermore, the model is validated against experimental and numerical data found in the open literature. The numerical predictions are compared against an adiabatic single-phase flow manifold system working with water and also against a two-phase flow upwardly oriented manifold system working with carbon dioxide. In addition to this, a numerical comparison of a manifold system with two different orientations is carried out. Concluding remarks about the possibilities that this kind of model offers are presented in the last section.