The survival of dipterocarp seedlings in the understorey of south-east Asian rain forests is limited by their ability to maintain a positive carbon balance. Photosynthesis during sunflecks is an important component of carbon gain. Field measurements demonstrated that Shorea leprosula seedlings in a rain forest understorey received a high proportion of daily photon flux density at temperatures supra-optimal for photosynthesis (72% at ≥30 °C, 14% at ≥35 °C). To investigate the effect of high temperatures on photosynthesis during sunflecks, gas exchange and chlorophyll fluorescence measurements were made on seedlings grown in controlled environment conditions either, under uniform, saturating irradiance (approximately 539 µmol m−2 s−1) or, shade/fleck sequences (approximately 30 µmol m−2 s−1/approximately 525 µmol m−2 s−1) at two temperatures, 28 or 38 °C. The rate of light-saturated photosynthesis, under uniform irradiance, was inhibited by 40% at 38 °C compared with 28 °C. However, during the shade/fleck sequence, photosynthesis was inhibited by 59% at 38 °C compared with 28 °C. The greater inhibition of photosynthesis during the shade/fleck sequence, when compared with uniform irradiance, was driven by the lower efficiency of dynamic photosynthesis combined with lower steady-state rates of photosynthesis. These results suggest that, contrary to current dogma, sunfleck activity may not always result in significant carbon gain. This has important consequences for seedling regeneration processes in tropical forests as well as for leaves in other canopy positions where sunflecks make an important contribution to total photon flux density.