Capsicum chinense, commonly known as the habanero pepper, is renowned for its culinary and medicinal value due to a great abundance of polyphenolic compounds. The pursuit of eco-friendly methods for extracting these metabolites, which produce high-purity extracts applicable to the food and pharmaceutical sectors, has led to the adoption of green technologies such as supercritical fluid extraction (SFE). In this methodology, by manipulating factors like temperature, pressure, and extraction time, the goal of producing extracts with elevated phenolic content from plant materials can be achieved. In this study, a central compound design (CCD) was conducted with the response surface methodology (RSM) to optimize the extraction of polyphenols from Capsicum chinense using supercritical fluids. The optimal conditions for total polyphenol extraction were determined as 63.1 °C, 1161.82 psi, and an extraction time of 132 min, with a total polyphenol content (TPC) of 1870 mg of gallic acid equivalent (GAE)/100 g extract. Additionally, concentration of several individual polyphenols were optimized, including catechin (236.27 mg/100 g extract, 62.8 °C, 1150 psi, and 132 min), chlorogenic acid (447.08 mg/100 g extract, 63.1 °C, 1150 psi, and 131.9 min), vanillic acid (136.38 mg/100 g extract, 41.9 °C, 1150 psi, and 132 min), diosmin + hesperidin (92.80 mg/100 g extract, 63 °C, 3200 psi, and 132 min), rutin (40 mg/100 g extract, 63.03 °C, 3200 psi, and 132 min), among others. These findings highlight the potential of supercritical fluid extraction for obtaining high yields of polyphenols from Capsicum chinese. The use of SFE-RSM also may optimize the extraction of specific phenolic compounds, and at the same time, it provides valuable insights for the development of extracts with enhanced bioactive properties for various applications in the food and pharmaceutical industries.