N-hydroxyphthalimide (NHPI) is an organocatalyst for free-radical processes able to promote the aerobic oxidation of a wide range of organic substrates. In particular, NHPI can catalyze the hydroperoxidation of polyunsaturated fatty acids (PUFA). This property could be of interest for biological applications. This work reports the synthesis of two β-cyclodextrin derivatives (CD5 and CD6) having a different degree of methylation and bearing a NHPI moiety. These compounds, having different solubility in water, have been successfully tested for the hydroperoxidation of methyl linoleate, chosen as the PUFA model molecule.