Background: Cimicifuga foetida L. is a perennial herbaceous plant belonging to the family Ranunculaceae and is distributed in temperate regions of East and Central Asia. The plant has traditionally been used in traditional medicine for the treatment of various disorders. Phytochemical studies have demonstrated the presence of biologically active compounds, including triterpenoid saponins, phenylpropanoids, flavonoids, phenolic compounds, and alkaloids. However, studies on the biologically active constituents and optimal extraction conditions of C. foetida growing under the environmental conditions of Mongolia remain limited. Aim: To identify selected biologically active compounds present in the aerial parts of Cimicifuga foetida L. and to determine the optimal conditions for extraction. Materials and Methods: The aerial parts of Cimicifuga foetida L., collected in August 2025 from the Gorkhi-Terelj area of Nalaikh District, were used as the study material. Biologically active compounds were identified by histochemical methods using potassium dichromate, ferric chloride, methylene blue, Lugol’s solution, Dragendorff’s reagent, and thymol–concentrated sulfuric acid reagent. Optimal extraction conditions were evaluated by extracting raw materials of 1, 2, and 3 mm particle sizes with 20–80% ethanol and determining the total polyphenol content using the Folin–Ciocalteu spectrophotometric method. Maceration, an intensified maceration method using agitation, percolation, and ultrasound-assisted maceration were also compared. Result: Histochemical analysis showed positive reactions for phenolic compounds, flavonoids, alkaloids, starch, and polysaccharides, whereas the reaction for essential oils was negative. The highest total polyphenol content (0.742%) was observed in the extract prepared from 2 mm particle-size material using 60% ethanol, while the lowest content (0.03882%) was observed in the extract prepared from 3 mm particle-size material using 20% ethanol. Among the extraction methods evaluated, ultrasound-assisted maceration produced the highest extractable matter content (38.3 ± 0.66%). The yield of the concentrated extract obtained using 60% ethanol was 15%, with a total polyphenol content of 0.43325%. Conclusion 1. Positive histochemical reactions for phenolic compounds and flavonoids, as well as alkaloids, starch, and polysaccharides, were observed in the transverse sections of the stems of Cimicifuga foetida L., whereas the reaction for essential oils was negative. 2. The optimal extraction conditions for Cimicifuga foetida L. raw material were determined to be a particle size of 2 mm, extraction with 60% ethanol, and an ultrasound-assisted intensified maceration method.