The marine isotopic stage (MIS) 5e marine terrace, a paleo-sea-level indicator, is widely distributed at Cape Shiriyazaki, which is located at the northeastern end of Shimokita Peninsula, NE Japan. The elevation of the inner edge of the marine terrace indicates a relative uplift at the site during late Quaternary. However, the marine terrace surface in the study area is covered with colluvium, loess, and soil. Therefore, to reveal the 3-dimensional structure of horizons buried under cover sediments, ground penetrating radar (GPR) profiling was performed across and in parallel to the inner edge on the ground surface. The GPR survey area is about 100 m across the inner edge and about 200 m in parallel to the inner edge. Impulse GPR profiling was carried out along nine survey lines above a depth of about 5 m, and stepped frequency modulated continuous wave (FMCW) GPR profiling along nine lines above a depth of about 8 m. GPR data were collected with common-offset modes using the 350 MHz GPR system (Koden Electronics Co., Ltd) for impulse GPR profiling and the 5-160 MHz FMCW GPR system (Kawasaki Geological Engineering Co., Ltd) for FMCW GPR profiling. Furthermore, to estimate the electromagnetic wave velocity used for depth-conversion of GPR sections, the common mid-point (CMP) ensemble composed of 31 scan data was acquired at the site, located at the center of the survey area, with wide-angle measurements. As a result of geological interpretations of depth-converted GPR sections after careful data processing, we obtained the 2-dimensional structures of the boundary horizons between the loess and gravel bed, and the horizons between the gravel bed and bedrock on all GPR sections. We constructed 3-dimensional structures of horizons using these 2-dimensional structures. The form of the top of the gravel bed is similar to the ground surface with the exception of a few small areas. Although the top of the bedrock dips a little toward the present coast, the form is almost horizontal. The top of the bedrock probably shows a surface of an uplifted wave-cut platform. The elevations of inner edges inferred from the ground surface, the top of the gravel bed (the bottom of the loess), and the top of the bedrock (the surface of uplifted wave-cut platform) are 32–34 m, 30–32 m, 28–29 m, respectively.