The puerarin-loaded lipid nanocapsules (PUE-LNCs), composed of labrafac, lipoid and water, were prepared with a phase inversion procedure. The formulation was optimized by simplex lattice design and characterized for its size, zeta potential and in vitro drug release. The results showed that the PUE-LNCs performed a homogeneous typical core-shell structure under transmission electron microscope (TEM). The entrapment efficiency and drug loading were 56.61 ± 0.27% and 2.62 ± 0.12%, respectively. In vitro drug release revealed the PUE-LNCs showed a controlled-release manner in both artificial simulated gastric juice (pH 1.0) and artificial simulated intestinal fluid (pH 6.8). Based on the aforementioned results, it should now allow a promising tuning for further applications of LNCs as a drug delivery system for puerarin.