Short-chain fatty acids play an important role in the physiology and metabolism of the colon. Disturbed balance of such compounds in human gut can significantly contribute to etiological factors of various gastrointestinal disorders and it may also increase the risk of developing cancer or cardiovascular diseases. The aim of the study was to select the optimal parameters for acetic, propionic and butyric acids extraction from stool samples. The experimental conditions were optimized with respect to the solvent sample shacking time, sample ultrasounds (Ultrasound-Assisted Extraction, UAE) exposure time and the number of extractions from the particulate stool samples. The screening of experimental parameters was conducted with fractional factorial design of experiments, namely 33–1. The optimal conditions for UAE were found, namely ultrasound digestion time of 40 min (at 35 °C), shaking time of 4 min, and the three subsequent extractions.