Stemflow (SF) is essential for water resources within forest ecosystems and can constitute up to half of the gross rainfall (GR), depending on the forest stand structures in coniferous plantations. Although numerous studies on SF yield have been reported globally for various forest types, very few studies on SF have been reported to examine the influence of forest stand structures on SF in Korea. This study aimed to quantify the relationship between SF and forest stand structures in unmanaged Japanese cypress plantations. Two study plots were established (10 m × 10 m each) in plantations with the same stem density (SD: 2500 stems ha-1) (hereafter P1 and P2). Almost all forest stand structures (canopy projection area, tree height, diameter at breast height (DBH), number of live and dead branches, and ratio of canopy length to canopy width), including canopy volume using mobile LiDAR devices, were investigated. To evaluate the efficiency of funneling rainwater for the effect of tree biomass on SF, a funneling ratio (FR) was used. The present SF ratios (20.7% in P1 and 22.3% in P2) were much higher than those reported in previous studies of various forest types in Korea (SF ratios: 0.2–5.8% with a mean of 2.0%). This is due to the interaction between the high SD and many under-canopy dead branches. Individual-scale FR was correlated with DBH (R2 = 0.43). The present stand-scale FRs (FRstand) (22.3 in P1 and 29.2 in P2) were much higher than those reported in the previous studies (FRstand: 1.0–33.3 with a mean of 7.8) because of the negative relationship between FRstand and mean DBH (R2 = 0.78, p = 0.02). Our results provide useful information for understanding changes in SF caused by forest stand structures.