Hyperbranched poly(ethylene imine) (PEI) with its high amino content is a versatile functional polymer that is widely used as a gene delivery vector in biological applications and as a ligand and precursor for ion exchange resins and membranes in water purification and metal recovery. We report here the first fully atomistic model of a 25 kDa hyperbranched PEI macromolecule. We utilized this model to carry out molecular dynamics (MD) simulations with explicit water molecules and chloride ions to study pH-dependent conformational changes. We find that growing the PEI macromolecule sequentially from the monomers yields atomistic structures whose sizes (radius of gyration) are in good agreement with the small angle neutron scattering experiments. Our analysis of the structural properties from MD simulations shows that conformations of the hyperbranched PEI exhibit oblate ellipsoidal elongation at low pH compared to high or neutral pH but with no significant changes in the corresponding sizes. This fully atomistic model of a 25 kDa hyperbranched PEI macromolecule in water provides much needed detailed atomistic information for advancing our fundamental understanding of the structures and host−guest properties of PEI-based functional reagents and materials for biomedical and sustainability related applications.