Hempseed protein isolate (HPI) has drawn significant attention as a promising source of plant-based protein due to its high nutritional value. The poor functionality (e.g., solubility and emulsifying properties) of HPI has impeded its food application for years. This study provides important new information on hempseed protein extraction, which may provide further insights into the extraction of other high-thiol-based plant proteins to make valuable plant-based products with improved functional properties. In this study, HPI was produced from hempseed meals using the AE-IEP method. The underlying mechanisms and extraction kinetics were investigated under different experimental conditions (pH 9.0–12.0, temperature 24–70 °C, and time 0–120 min). The results suggested that disulphide bond formation is an inevitable side reaction during hempseed protein extraction and that the protein yield and the free -SH content can be influenced by different extraction conditions. A high solution pH and temperature, and long extraction time result in increased protein yield but incur the formation of more intermolecular disulphide bonds, which might be the reason for the poor functionality of the HPI. For instance, it was particularly observable that the protein solubility of HPI products reduced when the extraction pH was increased. The emulsifying properties and surface tension data demonstrated that the functionality of the extracted hempseed protein was significantly reduced at longer extraction times. A response surface methodology (RSM) optimization model was used to determine the conditions that could maximise HPI functionality. However, a three-fold reduction in protein yield must be sacrificed to obtain the protein with this high functionality.