Air samples were collected at Mt. Fuji Research Station (FRS) for the measurements of volatile organic compounds (VOCs) in the summers of 2015 and 2016. In this study, 24 compounds were analyzed, of which only 12 halocarbons were quantified in 2015. The average total concentrations of target VOCs were 2.62 ± 1.38 and 2.99 ± 0.95 ppb in 2015 and 2016, respectively. The concentrations of individual VOCs ranged from a few ppt to a few ppb, indicating a highly inhomogeneous feature at the FRS. A cluster analysis of 3-day backward trajectories was performed for the sampling time. Except for the aromatic compounds, the VOCs showed relatively low concentrations in association with air masses originating from the coastal region in the low latitudes (15°N–35°N) of East Asia in 2015. By contrast, the clusters with elevated VOC concentrations mainly came from the high latitudes (35°N–60°N) of the Asian continent in 2016. No particular diurnal pattern was found for VOCs and CO, which might have resulted from suppressed mountain-valley winds at the FRS. Halocarbons regulated by the Montreal Protocol showed low variability and were in favorable agreement with background values at the Gosan station (GSN) and those reported in the literature. Other partially halogenated compounds with higher variability, such as CH3Cl and CHCl3, showed discrepancies at the FRS and GSN. 1,2-dichloroethane (R-150), 1,1-dichloroethane (R-150a), and 1,4-dichlorobenzene (p-DCB) were also measured at the FRS with concentrations of 24 ± 14, 38 ± 13, and 13 ± 10 ppt, respectively, in 2015. A close relationship between n-pentane and i-pentane with R2 more than 0.85 was found in both 2015 and 2016. Low ratios of n/i-pentane ranging from 0.25 to 0.67 were observed in the free troposphere at the FRS, comparable to most mountain stations.