Durability and safety of concrete structures are fully governed by mechanical properties. This is especially true at early age, when cement matrix is not yet fully developed, and phase arrangement becomes critical for understanding mechanical behavior. This factor can be thoroughly examined only with the use of numerical models. This study is specifically focused on the prediction of effective elastic properties of cement paste by Finite Element method (FEM) based on its microstructure. The 3-D microstructure is an output of a vector microstructural model. Up to 5 million of overlapping spheres can exist in the computational volume of cement paste. The geometrical representation for FEM computation therefore becomes a challenge. In this study, at first, specific aspects of the FEM are investigated with respect to the early age microstructure. Mesh for such a complex microstructure poses a challenge, simplifications of the geometry have to be accepted. Sensitivity to mesh type, resolution, integration scheme and size of computational volume is tested. The most important factor in the prediction is identified as artificial connectivity, which is a result of insufficient resolution. It causes substantial overestimation of elastic properties at the beginning of hydration. A scheme to partially treat this effect is presented. In the second part of the work, the model is applied to study variations of microstructural parameters. These include the effect of flocculation, water/cement ratio, particle size distributions and number of hydrate clusters. It is shown, that the model is able to capture the differences in microstructural arrangements despite the resolution limitations, verified experimentally. As such, the model has the capability to be used for explanation of anomalies in the material structure.