Recovery and chemical purification of Mo-98 from graphite collector which was separated by EMIS were made for the first time in Iran. In this research work, metallic Mo-98 isotope deposited on the internal surface of graphite was separated from pocket by scraping. Then, carbon was removed from the mixture of molybdenum and graphite by burning at 850oC in oxygen atmosphere in the form of CO2 and molybdenum was converted to oxide form (MoO3). Molybdenum tri-oxide was dissolved in hot and concentrated ammonia solution. In alkaline condition, the major impurity of Fe as hydroxide form was precipitated. In the next step, after acidifying the solution by sulfuric acid, a-benzoin oxime was added, and molybdenum organometalic complex was formed. The complex was filtrated, dried and ignited at 500oC in electrical furnace. Finally, 98MoO3 was obtained. The crystalline structure of MoO3 was confirmed by X-ray Diffraction (XRD) and its chemical purity of 97.44% was determined using the ICP-emission spectrometer.