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The protozoan cysteine proteases cruzain in Trypanosoma cruzi and rhodesain in Trypanosoma brucei are therapeutic targets for Chagas disease and Human African Trypanosomiasis (HAT), respectively. A benzimidazole series was previously characterized as potent noncovalent competitive cruzain and rhodesain inhibitors with activity against trypanosomes. Common structure–activity relationships (SAR) trends and structural modifications leading to selectivity against each enzyme were described. However, some of these trends could not be understood based on the reported binding mode of lead compound 1. Therefore, we employed microsecond molecular dynamics simulations and free energy calculations to understand qualitative SAR trends and to quantitatively recapitulate them. Simulations revealed the most stable protein–ligand interactions and provided insights concerning enzyme selectivity. Calculated relative binding free energies of compound 1 analogs exhibited deviations of 1.1 and 2.2 kcal/mol from the experimental values for cruzain and rhodesain, respectively. These data encourage prospective thermodynamic integration (TI) studies to optimize this series and facilitate the prioritization of compounds for synthesis.