An understanding of the mechanical behavior of polymeric materials is crucial for making advancements in the applications and efficiency of nanocomposites, and encompasses their service life, load resistance, and overall reliability. The present study focused on the prediction of the mechanical behavior of biopolymeric nanocomposites with nano-clays as the nanoadditives, using a new modeling and simulation method based on Comsol Multiphysics software 6.1. This modeling considered the complex case of flake-shaped nano-clay additives that could form aggregates along the polymeric matrix, varying the nanoadditive thickness, and consequently affecting the resulting mechanical properties of the polymeric nanocomposite. The polymeric matrix investigated was biopolyamide 11 (BIOPA11). Several BIOPA11 samples reinforced with three different contents of nano-clays (0, 3, and 10 wt%), and with three different nano-clay dispersion grades (employing three different extrusion screw configurations) were obtained by the compounding extrusion process. The mechanical behavior of these samples was studied by the experimental tensile test. The experimental results indicate an enhancement of Young’s modulus as the nano-clay content was increased from 0 to 10 wt% for the same dispersion grades. In addition, the Young’s modulus value increased when the dispersion rate of the nano-clays was improved, showing the highest increase of around 93% for the nanocomposite with 10 wt% nano-clay. A comparison of the modeled mechanical properties and the experimental measurements values was performed to validate the modeling results. The simulated results fit well with the experimental values of Young’s modulus.