As climate change progresses, it is becoming more crucial to understand how timber species respond to increased drought frequency and severity. Photosynthetic traits in a 40-year-old clonal Japanese cedar (Cryptomeria japonica) plantation were assessed under artificial drought stress using a roof to exclude rainfall and a control with no exclusion. C. japonica is a commercial tree that is native to Japan and has high growth on mesic sites. The maximum carboxylation rate (Vcmax), maximum electron transfer rate (Jmax), and dark respiration rate (Rd) in current-year shoots in the upper canopy were determined from spring to autumn over two growing seasons. In addition, the photosynthetic rate at light saturation (Pmax), stomatal conductance (gs), and intrinsic water use efficiency (WUEi) were measured in the morning and afternoon during the same period. Leaf mass per unit area (LMA) and nitrogen concentration (N) were also measured. The values of Vcmax, Jmax, Rd, N, and LMA did not differ between the two plots. By contrast, significantly lower Pmax and gs and higher WUEi were found in the drought plot, and the reduction in Pmax was accompanied by low gs values. Midday depressions in Pmax and gs were more pronounced in the drought plot relative to the control and were related to higher WUEi. Under drought conditions, mature Japanese cedar experienced little change in photosynthetic capacity, foliar N, or LMA, but they did tend to close the stomata to regulate transpiration, thus avoiding drought-induced damage to the photosynthetic machinery and improving WUEi.