This paper adopts a three-dimensional (3D) finite element method to simulate the injection molding of organic 3D stacked-chip assemblies. The geometry model of the assembly is simplified to a five-layered structure of stacked-chips with no solder bumps. The injection molding process incorporates 3D stacked-chip packaging and encapsulation techniques, and comprises primarily of multi-layer cavity-filling and reactive-thermosetting curing processes. The current investigation considers the effects of specifying different entrances on the resultant flow fronts, air-traps, and weld-lines. In general, the present results confirm the value of performing numerical simulations of the 3D stacked-chip packaging process to support the injection molding CAE approaches which are commonly applied nowadays to improve the packaging assembly design and to facilitate the rapid set up of mass-production conditions. The simulation results indicate that the best packaging results are obtained when the melt is introduced either at the center of the periphery side of the stacked-chip modulus or at its corner.