The large and untapped resources of chemical compounds with significant medical potential found in medicinal plant species make them valuable as sources for biomedicine. Traditional medical systems like Ayurveda and Chinese Traditional Medicine are just two of the many that use the essential medicinal plant Cassia fistula L. It is a medium-sized tree that loses its leaves in the autumn. Its name is from its beautiful yellow flowers and long, rod-shaped seeds with pulp inside. The plant's roots were extracted using petroleum ether, chloroform, alcohol, and water in that order, and the products were looked at for preliminary phytochemical screening and antioxidant activity. Analysis of phytochemicals like alkaloids, flavonoids, carbohydrates, glycosides, protein, amino acids, saponins, and triterpenoids showed that most elements were present. Furthermore, this work concentrated on isolating and purifying aloe-emodin and Physcionusing column chromatography and then determining their purity using HPTLC. Different extraction solvents were tested, and ethanolic produced the highest yield of both. Toluene: Ethyl acetate: Methanol at 5:4:1 (v/v) showed superior resolution of Rf values at 0.7 and 0.9 as aloe-emodin and Physcion, respectively. Different solvents with different polarities were tried before using TLC to separate aloe-emodin and Physcion. The Toluene-ethyl acetate-formic acid ratio was increased when the silica gel column chromatography polarity was applied to the alcohol extract.