Lake Kawaguchi is the second largest lake (area = 5.7 km²) in the Mount Fuji volcanic region and is located at the northern foot of Mount Fuji at 830.5 m above sea level. A borehole core of 88 m length (KA-1; 35°30.427'N, 138°43.701'E) was recovered from the western part of the lake between 1998 and 2000. The upper 15 m of the core mainly consists of silty sediments with intercalated scoria fallout deposits from Mount Fuji over the last ca. 18 kyr. The core also includes a fine-grained white pumice layer at 399.0 cm depth, which correlates with the Amagi Kawagodaira tephra (Kg), based on its geochemical composition and refractive index. We performed compound-specific radiocarbon analyses of fatty acids, as well as conventional ¹⁴C analyses of terrestrial macrofossils from core KA-1 to determine the depositional age of sediments based on ¹⁴C age of fatty acids and evaluate their potential as a dating tool for lake sediments. The dataset includes radiocarbon ages of fatty acids and plant leaves and geochemical composition of Kg from core KA-1.