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Most of the e-government projects fail. The unreliability in e-government system is very high. There are many reasons for failure but among them lack of interoperability is one of them. The interoperability is one of the prime features of electronic government system. It helps one system to interact with another system. It integrates all the required entities in the common domain. Enterprise architecture is one approach of providing interoperability among the different systems. EA provides a unified standard at the different levels of a system. This paper discusses on use and challenges of EA in developing countries. It also provides the solution of the challenges and the approach of reducing the failure rate of e-government system. It has considered the case of Nepalese context which is applied in all developing countries, especially in South Asia.