Conventional methods for determining the hydraulic properties of unsaturated soil are laborious and time consuming. Although the inverse method can be an effective alternative, it occasionally produces nonunique solutions. The problem becomes more difficult when the inverse method is applied to vertically heterogeneous soil profiles. This study evaluated the method proposed by Kosugi and Nakayama, which estimates retention and hydraulic conductivity functions simultaneously for each horizontal layer of a vertically heterogeneous soil using transient matric pressure profiles. Artificial rainfall experiments were conducted on an undisturbed forest soil sample, and 14 unknown parameters that are contained in both retention and conductivity functions were estimated for seven layers. The estimated hydraulic properties corresponded well with those measured using conventional methods. Various initial parameter guesses converged at very similar final parameters, indicating the unique, stable solution. In addition, the effects of model selection, the soil pore tortuosity parameter, and experimental errors on the estimation results are discussed.