Background: Boswellia carteri Bridw. is being widely used for its anti-inflammatory properties, as well as for wound healing, antimicrobial, and immunomodulatory properties, and boswellic acids (BAs) are considered to be the main active constituents. Objectives: To investigate optimal conditions of stir-baking process for the resin of B. carteri with vinegar of using response surface methodology (RSM). Materials and Methods: The concentration of acetic acid, heating temperature, and heating time were set as influential factors, and the yields of chemical compounds were the response values which were optimally designed by a Box–Behnken design. The amounts of 11-keto-β-boswellic acid (KBA) and α-boswellic acid (αBA) in B. carteri resin were quantified using high-performance liquid chromatography analysis. Results: Maximum amounts of KBA and αBA in B. carteri resin were obtained using 6% acetic acid for 10 min at 90°C in preliminary test. Two factor interactions, such as acetic acid concentration–heating temperature and heating temperature–heating time, were significantly observed by multiple regression analysis. Optimal processing conditions from RSM were 5.83% for acetic acid concentration, 9.56 min for heating time, and 89.87°C for heating temperature. Under the modified conditions, the experimental value of the response was 11.25 mg/g, which was similar to the predicted value. Conclusions: The results suggest that the optimal conditions for the stir-baking process of B. carteri resin were determined by RSM, which was reliable and applicable to practical processing of herbal medicine.