Optimization of pectin extraction from cocoa pod husk was carried out to examine independent variables that affect the quality of pectin obtained and determine the best conditions for the extraction process. In this study, three independent variables thought to contribute to microwave-assisted pectin extraction were used, namely, extraction time (20, 25, and 30 min), microwave power (180, 300, and 450 W), and citric acid concentration (2.5%, 5%, and 10%). Response surface methodology was applied using central composite design (CCD) to examine the effect of independent variables on the parameter measured. Among the seven parameters measured, namely, yield, temperature, moisture content, ash content, equivalent weight, methoxyl content, and galacturonic acid content, the statistical analysis test showed that the model equations that were suitable for predicting response values were temperature, moisture content, and ash content. Therefore, the optimization of conditions was only reviewed for these three parameters. Optimization results concluded that the factors that had the most significant effect on temperature, moisture content, and ash content were extraction time and microwave power. Optimal conditions for pectin extraction were at 30 min extraction time, 450 W microwave power, and 10% solvent concentration, resulting in a temperature of 104 °C, moisture content of 6%, and ash content of 8%. Other parameter values measured under these conditions were a yield of 21.10%, equivalent weight of 602.40 mg/mol, methoxyl content of 6.07%, and galacturonic acid content of 72.86%. Pectin extracted from cocoa pod husk using this method has the potential to be further applied, especially in the food and pharmaceutical industries.