Mubaje was born in Bungokho in Mbale district. He became familiar with Islamic affairs early in his life, thanks to the years spent in a Madras Islamic Primary School in Natete Kayunga district and Namatembe Islamic Institute in Namutumba. Mubaje later joined Bugembe Islamic Institute in Jinja, where he completed senior six in 1976 in Islamic studies. In 1977, he went to Riyad in Saudi Arabia for a bachelor’s degree in Sharia (Islamic law). In 1981, he became the Imam of Madinah Mosque, Mbale and founded Mahdi Noor Islamic Institute.

Months later, he became the Mbale district khadi, while pursuing a post-graduate diploma in philosophy at Mbale Islamic University. Mubaje later enrolled at Makerere University for a master’s degree in religious studies. After graduation, he returned to Mbale University as a lecturer in religious studies.

In 2000, Dr. William Vendley and Sheikh Shaban Mubaje met and formed the Interreligious Council of Uganda-RfP. Sheikh Shaban Mubaje used the platform of Religions for Peace International to begin to speak out and address rebel groups in Uganda by preaching the message of love and coming together despite different religious beliefs. In the same year, he was unanimously elected Grand Mufti, of Uganda.

Since the Inter-Religious Council of Uganda was formed, Sheikh Shaban Mubaje has continued his relentless work with Religions for Peace. In 2001, he helped form the Religions for Peace-African Council of Religious Leaders, where he has facilitated the involvement of Muslim communities in Pan-African development initiatives. He continues to hold the position of Co-Chair of the Council.

In 2015, he became a member of the Supreme Council of Muslim Leaders, a global assembly of Muslim scholars.