Subcritical water extraction (SWE) is a green technology with interesting advantages, including a cheap and selective process for various applications, including the extraction of bioactive compounds. However, knowledge and data on upscaling from studies related to this process are limited. Therefore, this study reports comparative experimental data for the upscaling process of subcritical water extraction. Two SWE processes with different scales, namely the commercially available high-pressure system ASE 200 with a capacity of 28 ml and a locally fabricated high-volume SWE process with a capacity of 1000 ml, were employed for the extraction of medicinal compounds from Zingiber officinale, namely 6-gingerol and 6-shogaol. The effect of temperature for both setups on the compounds' concentrations was studied from 130°C to 200°C at a constant pressure of 3.5 MPa and for a duration of 30 minutes. The quantitative analysis for each compound was performed using High-Performance Liquid Chromatography (HPLC). The optimum temperature for the extraction of 6-gingerol using the high-volume SWE was 130°C, with a concentration of 1741.54 ± 0.96 µg/g, which differs from ASE 200, in which the optimum extraction temperature for 6-gingerol was 140°C, with a concentration of 1957.22 ± 2.55 µg/g. Meanwhile, for the extraction of 6-shogaol, both pieces of equipment recorded the same optimal temperature—170°C—with concentrations of 541.78 ± 3.16 µg/g and 1135.23 ± 1.18 µg/g for high-volume SWE and ASE 200, respectively. This is possibly due to the difference in the scale of the extraction process, which was up to 35-fold, from a 28 ml to a 1000 ml capacity, consequently affecting the heat and mass transfer processes during extraction. Thus, scale-up factors need to be considered for effective design during the scaling up of the SWE process to obtain higher mass transfer efficiency.