Plain or coated pellets of different densities 1.45, 2.53, and 3.61 g/cc in two size ranges, small (380–550 μm) and large (700–1200 μm) (stereoscope/image analysis), were prepared according to experimental design using extrusion/spheronization. Multiple linear regression (MLR) and artificial neural networks (ANNs) were used to predict packing indices and capsule filling performance from the “apparent” pellet density (helium pycnometry). The dynamic packing of the pellets in tapped volumetric glass cylinders was evaluated using Kawakita’s parameter a and the angle of internal flow θ. The capsule filling was evaluated as maximum fill weight (CFW) and fill weight variation (FWV) using a semi-automatic machine that simulated filling with vibrating plate systems. The pellet density influenced the packing parameters a and θ as the main effect and the CFW and FWV as statistical interactions with the coating. The pellet size and coating also displayed interacting effects on CFW, FWV, and θ. After coating, both small and large pellets behaved the same, demonstrating smooth filling and a low fill weight variation. Furthermore, none of the packing indices could predict the fill weight variation for the studied pellets, suggesting that the filling and packing of capsules with free-flowing pellets is influenced by details that were not accounted for in the tapping experiments. A prediction could be made by the application of MLR and ANNs. The former gave good predictions for the bulk/tap densities, θ, CFW, and FWV (R-squared of experimental vs. theoretical data >0.951). A comparison of the fitting models showed that a feed-forward backpropagation ANN model with six hidden units was superior to MLR in generalizing ability and prediction accuracy. The simplification of the ANN via magnitude-based pruning (MBP) and optimal brain damage (OBD), showed good data fitting, and therefore the derived ANN model can be simplified while maintaining predictability. These findings emphasize the importance of pellet density in the overall capsule filling process and the necessity to implement MLR/ANN into the development of pellet capsule filling operations.