Having evaluated the operational method used for issuing the Musharakah sukuk of the Iranian central bank, this paper tries to shed lights on the Fiqhi (jurisprudential) and economic (financial) challenges of this instrument. For deriving the initial challenges, a desk research is conducted and for finalizing and ranking of challenges, the Delphi method is used in the society of Islamic banking experts in Iran. The results show that because of different shortcomings of the Iranian central bank Musharakah sukuk, the best choice for Iranian central bank is not to issue this kind of Sukuk for sake of open market operation. Instead, the central bank can enter in the secondary market of the governmental Sukuk and, by buying and selling of the sovereign securities, conduct open market operation. However, if the secondary market of the governmental Sukuk is not deep in the short-run and the central bank is obliged to issue its own securities, yet again, the Musharakah Sukuk is not the best choice and it is possible to issue other kinds of Sukuk like Ijarah Sukuk. The characteristics of Ijarah Sukuk are more suitable for open market operation.