High-throughput screening of dendrimer-binding drugs is essential for the design and optimization of dendrimer-based drug delivery systems. In this study, pulsed gradient spin echo (PGSE) NMR was used for fast screening dendrimer-binding compounds using common amino acids as a screening pool. Diffusion coefficients of the amino acids before and after the addition of poly(propylene imine) (PPI) dendrimer were used to rank the binding affinities of the amino acids to the dendrimer. Among the common amino acids, cysteine, glutamic acid, aspartic acid, and tryptophan show strong binding affinity to PPI dendrimer. Tryptophan forms inclusion complexes with PPI dendrimer through hydrophobic interactions, while other amino acids mainly bind with PPI dendrimer via ionic and hydrogen-bond interactions. The PGSE NMR-based screening method provides new insights into high-throughput screening of dendrimer-binding compounds and should facilitate the study of dendrimer-based host-guest systems.