Novel biocompatible systems suitable for the controlled release of active ingredients are under the spotlight within the last few years. The present investigation focuses on the preparation of nanoparticles (NPs) based on the amphiphilic copolymer pullulan‐graft‐poly(Z‐L‐lysine) bearing different amounts of lysine (10, 20, and 30 wt%), and on the evaluation of their ensuing viability to encapsulate the hydrophobic nonsteroidal anti‐inflammatory drug indomethacin (INDO). The copolymers are synthesized by ring‐opening polymerization, characterized by NMR and FTIR, and their critical aggregation concentration is determined by fluorescence. The NPs are prepared with and without INDO using different copolymer/solvent ratios and INDO/copolymer ratios. The hydrodynamic diameter and polydispersity of the NP suspensions are monitored by dynamic light scattering for 30 days. Their sizes vary between 208 and 338 nm, and some reach the micrometric range (19–73 μm). INDO‐free NPs are identified as spherical‐shaped by atomic force microscopy. Two formulations are tested in terms of encapsulation efficiency (EE = 43%–89%), and the drug crystallinity (DC = 7%–27%) which is determined by differential scanning calorimetry, indicating a reduction with respect to pristine INDO. The results suggest that the copolymers prepared herewith have potential to be applied as carriers for new drug delivery systems of class II drugs.