Muslim faith schools have been existent in the UK since the 1980s and their number has been rising ever since. These schools are established specifically to provide Muslim children with a learning environment based on Islamic values. However, fulfilling such a mission would not be an easy task in a globalised context characterised by secularism and materialism. The study reported in this paper sought to explore the leadership experiences and challenges as perceived by the head teachers of Muslim schools in the UK. The study employed a qualitative research design using semi-structured interviews with a sample of head teachers from four Muslim schools in London and Nottingham. The findings revealed that although the participating head teachers were proud of their role as leaders of Muslim schools, they faced significant challenges in their practice of leadership within British secular society. While some of these challenges were general in nature such as parental expectations and lack of support from Muslim community, other challenges were more practical and mission related such as negative perceptions among the wider society, issues in developing Muslim identity among students in a secular society, recruitment of qualified Muslim teachers and financial challenges.