The gas distribution uniformity between anode channels in an indirect internal reforming type molten carbonate fuel cell (MCFC) is a crucial design parameter that influences both the electrical performance and durability. In this paper, a three-dimensional computational fluid dynamics (CFD) analysis was performed to investigate flow characteristics in the anode channels and manifold where shape, pressure drop and channel temperature conditions were varied. The combined mesh consists of a hexahedral mesh in the channels and a polyhedral mesh in the manifold. Results indicate that rotational flow develops at the left and right sides of the anode manifold that induces an uneven mass flow rate distribution in the anode channels. Gas flow rate uniformity is enhanced as the depth of the manifold decreases, as the pressure drop in the anode channels increases and as the temperature difference between the indirect internal reforming (IIR) channels and anode channels decreases.