A small library of benzo[4,5]thieno[2,3‐d]pyrimidine phthalimide and amine derivatives was evaluated for inhibitory activity against dipeptidyl peptidase‐4 (DPP‐4). The phthalimide derivatives exhibited better activity than the amine precursors, with 2‐(2‐(3‐chlorobenzyl)‐5,6,7,8‐tetrahydrobenzo[4,5]thieno[2,3‐d]pyrimidin‐4‐yl)isoindoline‐1,3‐dione (compound 14) as the most effective inhibitor (IC50 = 34.17 ± 5.11 μM). The five most potent selected inhibitors did not show cytotoxicity to a greater extent on Caco‐2 cells, even at a concentration of 250 μM. Compound 14 is considered as a novel representative of the rare noncompetitive DPP‐4 inhibitors. Molecular docking and dynamics simulation indicated the importance of the Tyr547, Lys554, and Trp629 residues of DPP‐4 in the formation of the enzyme–inhibitor complex. These observations could be potentially utilized for the rational design and optimization of novel (structurally similar, with phthalimide moiety, or different) noncompetitive DPP‐4 inhibitors, which are anyway rare, but favorable in terms of the saturation of substrate competition.