Tulisan ini menggambarkan hasil studi kasus tentang pengembangan budaya toleransi keagamaan yang berlangsung pada SMA Muhammadiyah Kupang Nusa Tenggara Timur. Data dihimpun melalui wawancara dengan para guru, siswa dan kepala sekolah. Proses penelitian, termasuk studi literatur, observasi lapangan dan penulisan berlangsung mulai bulan Juli sampai Nopember 2012. Siswa SMA Muhammadiyah terdiri dari penganut Islam dan Kristen dan Katolik (Kristiani). Pengembangan budaya toleransi di SMA Muhammadiyah dilakukan sebagai bagian dari misi dakwah Islam yang inklusif, mencerdaskan siswa tanpa membedakan latarbelakang agama. Implementasi pengembangan budaya toleransi dilakukan dengan pendekatan budaya, yang bersifat adaptif dengan kondisi masyarakat sekitar sekolah yang beragama Kristiani. Pemahaman dan sikap toleransi antar siswa yang berbeda agama di SMA Muhammadiyah Kupang dikembangkan melalui proses intra dan ekstra kurikuler, sejak siswa masuk di sekolah Muhammadiyah. Hasilnya, siswa dari berbagai agama dapat bekerja sama, saling menghargai perbedaan agama, mengembangkan tradisi berdemokrasi di dalam dan di luar kelas. Di kelas, para siswa berbeda agama memperoleh pendidikan agamanya dan di ajarkan oleh guru yang seagama. Di luar kelas siswa didukung untuk mengadakan kegiatan keagamaan sesuai dengan agamanya masing-masing. Model pengembangan budaya toleransi di SMA Muhammadiyah dapat dipromosikan dan dijadikan sebagai contoh pengembangan budaya toleransi keagamaan untuk sekolah-sekolah yang sejenis. This paper describes the results of a case study of the development of a culture of religious tolerance in SMA Muhammadiyah Kupang of East Nusa Tenggara. Data was collected through interviews with teachers, students and principals. Research, including literature study, field observations and writing took place from July to November 2012. Students of SMA Muhammadiyah consist of adherents of Islam and Christianity, including Catholics. Development of a culture of tolerance in SMA Muhammadiyah was conducted as part of the inclusive mission of preaching Islam, to educate students regardless of religious background. Implementation of the development of a culture of tolerance is done with a cultural approach, which is adaptive to the conditions in surrounding, mostly-Christian communities. Understanding and tolerance among students of different religions in SMA Muhammadiyah Kupang is developed through a process of intra-and extra-curricular activities beginning when students enter school. As a result, students of various religions can work together, respect religious differences, and develop democratic traditions inside and outside the classroom. In class, students of different religions obtain their religious education from teachers who are of that same religion. Outside the classroom students are supported in conducting religious activities according to their respective religions. This model of the development of a culture of tolerance in SMA Muhammadiyah can be promoted and used as an example of religious tolerance for the cultural development of similar schools.