Abstract The natural circulation test (NCT) was conducted in the Phénix prototype French 580MWth sodium fast reactor (SFR) in 2009. The main goal of the Phénix NCT is to validate system- and CFD-codes with respect to the establishment of natural circulation in the primary system of a pool type SFR. The present paper describes the calculation of the NCT by coupling the 3D computational fluid dynamics (CFD) code TRIO_U with the best estimate thermal hydraulic system code CATHARE. The coupling methodology and the modeling at the system and at the CFD scales are first presented. A validation of the coupling methodology based on a coupled CATHARE/CATHARE calculation compared to the standard CATHARE predictions is then proposed. In a second step, the results of the TRIO_U/CATHARE calculation are compared both to the available experimental data and to the results of a CATHARE alone computation. These comparisons highlight the effectiveness of coupling CFD- and system-codes for the analysis of plant transients where three-dimensional phenomena play an important role.