The crustally guided shear wave, Lg, is typically the most prominent phase of a nuclear explosion at regional distance. This Lg phase is analyzed often to discriminate a nuclear explosion from a natural earthquake. In addition, the Lg phase allows us to determine the size of the detonation. A nuclear explosion test in North Korea was conducted on 9 October 2006. The epicenter was located close to the eastern shore of the Korean Peninsula, resulting in raypaths that vary significantly according to the azimuths. In particular, rays radiated in the southern direction experience lateral variation of crustal structures at the continental margin. We examine the influence of raypaths on regional seismic phases by comparing the spectra and waveforms from different raypaths. Three natural earthquakes in North Korea are also examined to determine the raypath effect. We find that the Lg from the nuclear explosion dissipated significantly as result of energy leakage into the mantle resulting from variations in crustal thickness along the portion of the raypath traversing the western tip of the Sea of Japan (East Sea). Some of the leaked energy develops into mantle lid waves (Sn), causing a large energy increase to Sn. A similar feature is observed in the records of natural earthquakes. This feature is confirmed by seismic waveform modeling. The raypath effect also causes underestimation of magnitude. The Lg body wave magnitude, mb(Lg), is estimated to be 3.8–4.2 for records from pure continental paths and 2.6–3.4 for records from paths crossing continental margins. This result illustrates the need to consider raypath effects for the correct estimation of magnitudes of regional events, including a nuclear explosion.