Background In India, cancer of the cervix is the second most common cancer in women. Nowadays, various traditional herbal formulations can be used as adjuncts during conventional cancer therapies due to their anticancer activity. Habbe Musaffi Khoon (HMK), a Unani compound formulation, is traditionally used as a blood purifier and thus used to treat boils, scabies, acne, and pimples. It is also indicated in skin diseases, Habis-ud-Dam (styptic), and therapeutically used in Nafz-ud-Dam (hemorrhagic). Objectives The main purpose of this work was to phytochemically characterize HMK aqueous extract (HMKaq) and determine its activity against cervical cancer cells. Materials and Methods HMKaq was subjected to liquid chromatography-mass spectrometry (LC-MS) and evaluated for the presence of phytocompounds. HMKaq was evaluated for its effect on the viability of cervical cancer cells (HeLa, SiHa, and C33A) and was determined by MTT assay. Trypan blue dye exclusion was used to determine the outcome of HMKaq on the growth kinetics of cervical cancer cells. The role of HMK in regulating the cell cycle was analyzed by FACS and its effect on apoptosis was evaluated by checking mitochondrial membrane potential readings of JC-1 aggregates on a microplate reader and on the mRNA expression of caspase-3 and cytochrome c was evaluated by PCR. Results LC-MS analysis revealed 3845 compounds, out of which 58 were the major compounds. These included phenolics, esters, fatty acids, furans, quinones, tannins, flavonoids, and terpenes. HMKaq reduced the viability and growth of the cells. It induced arrest in the cell cycle of HeLa and apoptosis in SiHa and C33A by depolarizing the membrane potential of the mitochondria and upregulation of mRNA expression of Cas3 and Cyt C. Conclusion HMK exhibited anticancer activity against cervical cancer cells, thereby signifying its therapeutic potential.