This research is aimed to investigate the factors affecting Mudaraba deposits on Islamic Commercial Bank in Indonesia using Fixed Effect Model (FEM) method in the panel data. Four variables, profit sharing rate, interest rate, GDP, and number of Islamic Commercial Bank’s branch offices, are thought to have influence on the volume of Mudaraba deposits. It uses quarterly time series in the period of 2004 – 2013. The research was conducted at Bank Muamalat Indonesia, Bank Syariah Mandiri, and Bank Mega Syariah Indonesia. The Result shows that the volume of Mudaraba deposits on Islamic Commercial Bank in Indonesia does not depend on profit sharing rate, interest rate, and the number of Islamic Commercial Bank’s branch office but depend on Gross Domestic Products (GDP). This research supported the view that in order to increase the volume of Mudaraba deposits in Indonesia, it is suggested that Islamic Banks are expected to add to its market share by entering the large corporate sector (SOEs and private enterprises upper middle) so that third-party funds, in particular Mudaraba deposits can and able to compete with Conventional Commercial Bank market share. Islamic Commercial Banks can thus optimally as executive financial intermediation for the financing and distribution on the real sector and not only focus on the retail sector and SMEs. Lastly, Islamic Commercial Banks in Indonesia should also provide a more branch offices of Islamic Commercial banks are built in order third-party funds and were able to distribute more optimally targeted at the real sector. The author suggest that the results of this study can add to the results of the study in order to develop Islamic Commercial Banking in Indonesia as well as to provide input related to policy measures in increasing deposits, especially deposits Mudaraba with the factors that influence it.