Background Guggulutiktam Kashayam (GTK) is a water decoction used in Ayurveda for the treatment of various diseases like skin diseases, ulcers, anemia, thyroid problems, stress, liver disease, and leucorrhoea. It is a polyherbal formulation prepared from specific parts of 28 medicinal plants. Objectives The study aimed at a comparative phytochemical evaluation of an important polyherbal formulation with its ingredient plants. Materials and Methods Chemical profiling of GTK has been carried out in comparison with its ingredient plants. Spectrophotometric estimation of major class compounds and high-performance thin-layer chromatography (HPTLC) profiling were done using a standardized protocol. Results The results of the study showed that the phytochemical contents of the finished formulation are different from those of the ingredient plants, which might be due to the numerous synergistic and antagonistic interactions of numerous chemical components extracted from different ingredient drugs. HPTLC-based comparative chromatograms showed the differences and similarities in certain compounds that are specific to some of the plant ingredients. Conclusion The study established the cumulative chemical interactions of various phytochemicals during the preparation of an important polyherbal formula used in Ayurveda.