The root of a ginseng-like plant named Codonopsis javanica is a valuable ingredient in folk medicine with diverse biological properties and has been used in treatments for various diseases, including leukemia, inflammation, and hepatitis. This study aimed to optimize various parameters related to the extraction process of C. javanica root (CJR) with respect to total phenolic content (TPC), total flavonoid content, and antioxidant activities of the obtained CJR extract. We first performed a series of single-factor investigations taking drying conditions and different extraction parameters such as material size, extraction solvent, solvent concentration, extraction temperature, material/solvent ratio, extraction cycle, and stirring speed as varying factors. Then, a response surface methodology procedure was adopted with a central composite design to optimize further the extraction process in order to maximize the TPC. We found that the use of convection drying at 70 °C for 8 hours gave the extract with the highest TPC and antioxidant activities. Optimal extraction parameters were found as follows: ethanol with a concentration of 56.0% as the solvent, material-to-solvent ratio of 1/38.0 g/mL, extraction time of 67.2 minutes, material size ≤0.5 mm, temperature 60 °C, through 1 extraction cycle, and with a stirring speed of 300 rpm. Under the optimized conditions, the experimental value for TPC was 2.9 mg gallic acid equivalent (GAE)/g dry weight (DW), which is reasonably close to the value predicted by the model (2.8 mg GAE/g DW). The half-maximal inhibitory concentration (IC50) values determined by the 2,2-diphenyl-1-picrylhydrazyl and 2,2′-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid free radical tests of the CJR extract obtained under optimal conditions were 1042.3 and 299.0 µg/mL, respectively.