The paper presents the results of theoretical calculations in terms of the G4MP2 composite method for cyprodinil–α-cyclodextrin (C ⁰@α-CD) and cyprodinil–β-cyclodextrin (C ⁰@β-CD) systems. Studies also covered analogous systems consisting of the anion (C ⁻) and the cation (C ⁺) of cyprodinil. The geometries of the cyprodinil molecule and ions were optimized on the basis of the DFT theory, using hybrid (B3LYP, PBE0), pure (B97-D) and “meta” (M06-2X) GGA functionals for selected Pople basis sets [6-311++G(d,p), 6-311++G(2d,p), 6-311++G(2d,2p)] and Dunning basis set (aug-cc-pVDZ). The research results suggest that the affinity of “guest” molecules for “hosts” is relatively low. Theoretical studies of the “guest-host” systems allow to predict the properties of the designed preparations.