The purpose of this article is to provide a narrative on the historical development of Muslim education with the objective of examining challenges and opportunities to support the strengthening of Muslim education agenda through policy dialogue and stakeholders' engagements. The paper utilizes methods of inquiry such as literature review, observation, and analysis. Key findings are that Kenyan national education is strongly controlled by the Christian missionaries. For example, the Catholic Church controls about 27% of the country's education. The country's education is still subjected to the various socioeconomic dynamics, where Muslim education is not the exception. The rights of Muslim students in the Mission institutions are extremely limited, allowing students only a special place for prayers. This is against country constitution and child rights in Kenya. The problem of historical discrimination continues to hurt Muslims to date as the government is yet to appreciate dualism in education in terms of policies and practices. In the earlier 1990s, the government refusal to register the Muslim teachers' college in Mombasa was practically evident and to date, the country continues to encounter an acute shortage of Islamic and Arabic teachers. Muslim parents remain the most worried as some of their children are subjected to the teaching of Christian religious education. The article calls for an urgent restructuring along with support for the work of the Muslim Education Council, with the objective of facilitating Muslim education policy development, database, curriculum development, training, research, and partnership. This will help transform the knowledge, thought, and practices among the Muslim learners. They must also fight examination corruption in Muslim-dominated areas by creating awareness, promoting capacity building, quality assurance, networking, benchmarking, research, and linkages in order to reach the desired center of excellence for Muslim educational institutions. The Council also must have a special relationship with the country's judiciary system in order to advance the rights of Muslim students in schools, colleges, and universities.