In this study, the unsteady behavior of the boundary layers developing on a low-pressure turbine (LPT) stator profile and their effect on secondary flow patterns in a 1.5-stage turbine configuration are investigated under the influence of periodic inflow perturbations. The experimental setup previously employed to analyze the unsteady secondary flow in the stator wake has been enhanced by hot-film sensor arrays placed on the stator profiles at different blade height positions to provide time-resolved data from within the passage. The stator inflow is perturbed by a rotating wake generator, and a modified T106 profile has been considered for the blading. The modified profile, labeled as T106RUB, was developed for matching the transition and separation characteristics of the popular original T106 profile at low flow speeds, thus facilitating measurements to be taken in a large-scale test rig with its improved accessibility. The transition phenomena occurring in the profile boundary layers are investigated under both unperturbed and periodically perturbed inflow by means of spectral analysis, the semi-quantitative characterization of the wall-stress system, and an evaluation of the statistic quantities. In particular, the periodic changes of the suction-side boundary layer flow region toward the trailing edge are studied in detail. Furthermore, time-resolved hot-film measurements at different blade height positions facilitate a detailed comparison of the quasi two-dimensional mid-span profile flow and the near end-wall profile flow, which is subject to the influence of secondary flow structures. These information are employed to assess to which extent the additional turbulence originating from the wakes affects the blade boundary layers and thus the secondary flow structures. Furthermore, the role of the perturbation frequency on the coupled system of boundary layers and secondary flow structures is evaluated.