We develop a lower critical field (Hc1) measurement system using the third-harmonic response of an applied AC magnetic field from a solenoid coil positioned above a superconducting sample. Parameter Hc1 is measured via detection of the third-harmonic component, which drastically changes when a vortex begins to penetrate the superconductor with temperature increase. The magnetic field locally applied to one side of the sample mimics the magnetic field within superconducting radio-frequency (SRF) cavities and prevents edge effects of the superconducting sample. With this approach, our measurement system can potentially characterize surface-engineered SRF materials such as Superconductor-Insulator-Superconductor multilayer structure (S-I-S structure). As a validation test, we measure the temperature dependence of Hc1 of two high-RRR bulk Nb samples and obtain results consistent with the literature. We also confirm that our system can apply magnetic fields of at least 120 mT at 4-5 K without any problem of heat generation of the coil. This field value is higher than those reported in previous works and makes it possible to more accurately estimate Hc1 at lower temperatures.