We evaluated the drug-encapsulation state of insulin (INS)-loaded liposome using a novel column-switching HPLC system that can automatically separate unloaded drug from encapsulated drug by hydrophobic interaction. When the INS-loaded liposome was dispersed in water (pH 7.4), the encapsulation efficiency (EE) obtained by the column-switching HPLC system was consistent with that obtained by a conventional ultracentrifugation method. However, the INS-loaded liposome dispersed in 0.1% acetic acid (pH 3.3) showed disagreement between the EEs obtained by both methods. Considering the results of particle size, zeta potential, and transmission electron microscope (TEM) observations, we hypothesized that the column-switching HPLC method was able to distinguish INS adsorbed onto the liposome surface from the encapsulated INS, although an ultracentrifugation method precipitated the adsorbed INS onto the liposome surface along with the encapsulated INS. Therefore, the novel column-switching HPLC system may be a more accurate and useful technique for characterization and optimization of the INS-loaded liposome formulation.