Cocrystallization has matured into an established technique for fine-tuning the physicochemical properties of active pharmaceutical ingredients (APIs). This technique has been adopted by pharmaceutical drug companies, with increasing numbers of cocrystal-based drug products now entering the market. Surprisingly, however, studies into the formulation aspects of cocrystal-based drugs are relatively few and far between compared to the vast literature on their design, synthesis, and characterization. We herein report the results of our investigations into cocrystal–excipient interactions in water that determine the dissolution properties of cocrystals in formulation by a combination of molecular dynamics (MD) simulation and experimental approaches. Two cocrystals of an antirheumatic drug, leflunomide (LEF) with 3-hydroxybenzoic acid (HBA) and 2-picolinic acid (PIC), were assessed in formulation with the frequently used excipients lactose and dibasic calcium phosphate (DCP). For comparison, the dissolution of neat LEF formulations with these excipients was also evaluated. The parameters deduced from MD simulations, such as solvent-accessible surface area, intermolecular hydrogen bonds among formulation ingredients and water, and interaction energy between the API (or cocrystal) and water were found to be essential indicators in the prediction of cocrystal formulation dissolution trends. It was found that the presence of lactose as an excipient improved the dissolution of the cocrystal formulation compared to the neat cocrystals, most notably for the LEF-PIC cocrystal. In contrast, DCP was seen to have a detrimental effect on the dissolution of cocrystal formulations, all exhibiting lower dissolution than their neat cocrystal counterparts and LEF. Careful analysis of these results revealed that the nature of the excipient plays a significant role in the dissolution properties. While the improved dissolution of the lactose formulations was attributed to its hydrophilic nature, the ionic and hydrophobic nature of DCP was likely responsible for its detrimental effect. The results of the MD simulations were found to be in excellent agreement with the experimentally observed dissolution hierarchy.