AbstractTree mortality by self‐thinning is an inevitable consequence of the long residence times of standing trees in unmanaged coniferous plantations. Stemflow (SF) is an important localized input of rainwater into the soil in forest ecosystems. However, little information is available on how tree mortality affects SF yields. We took weekly measurements from 16 trees in a 20 × 10 m plot containing 50 trees in a dense unmanaged Japanese cypress plantation from April to October 2017. These 16 trees were classified into two groups: standing‐live SF trees (n = 11, tree height [H]: 13.4 ± 1.1 m, DBH: 18.5 ± 3.8 cm, crown projection area [CPA]: 5.4 ± 0.8 m2, average ± standard deviation) and standing‐dead SF trees (n = 5, H: 7.9 ± 1.4 m, DBH: 10.0 ± 1.9 cm, CPA: 0.0 ± 0.0 m2). Because the smaller standing‐dead trees with no crown were all positioned under the canopy of standing‐live trees, the mean tree‐scale SF volume (SFVtree) of standing‐dead trees was approximately 10.3 times smaller than that of standing‐live trees. The much smaller SFVtree of standing‐dead trees was also explained by the basal area (3.5‐fold smaller) and the tree‐scale SF funnelling ratio (FRtree, 2.9‐fold smaller). SFVtree of standing‐dead trees was so small that the ratio of stand‐scale SF (SFstand) to gross rainfall (GR) (SFstand/GR) was similar regardless of whether standing‐dead trees were excluded or included (21.4% vs. 21.6%) in SFstand calculations, indicating that SFstand/GR could be reliably estimated using only standing‐live trees.