The novel Synergistic pharmaceutical composition for prophylactic treatment of migraine comprising of aqueous extracts of Sapindus trifoliatus and Emblica officinalis in combination with pharmaceutically acceptable selective additives and process for manufacturing the same. The formulation of the invention is stable and effective in prophylactic treatment of migraine. The Synergistic composition is obtained in the form of aqueous nasal drops for effective prophylactic treatment of migraine which would be safe without any harmful side effect and in particular would avoid/reduce chances of damage/irritation to the nasal mucus membrane when administered nasally. The present invention also provides for method of prophylactic treatment of migraine by administration of the Synergistic formulation comprising aqueous extract of Sapindus trifoliatus and Emblica officinalis in combination with selected pharmaceutically acceptable additives in the form of nasal drops.