The efficiency of hot water extraction (HWE) is dependent on the size of treated wood. While previous research regarding this size-effect has focused on HWE treating sawdust and wood chips, this study investigated its effect on wood blocks with precise dimensions and a broad range of treatment conditions. Scots pine (Pinus sylvestris L.) sapwood samples with dimensions of 10 × 10 × 20 mm3 and 25 × 25 × 50 mm3 (R × T × L) were HWE treated at 130–170 °C for 40–200 min using liquid-to-solid ratios of 4–20. Our results showed that wood mass loss, which was primarily caused by the decomposition of hemicelluloses, was larger when using small samples. This was mainly assigned to a higher quantity of acetone-soluble decomposition products that remained within the large samples, due to longer distances for diffusion and mass transfer from the wood blocks to the extraction liquid. In line with wood mass loss differences, the amount of dissolved compounds (i.e., carbohydrates) in the extraction liquid at different treatment severities was dependent on the wood size, while the liquid-to-solid ratio had only modest effects. However, composition changes of the extraction liquid, in particular changes in the proportion of poly- and monocarbohydrates with increasing treatment severity, were similar for both sample sizes.