Bosnia and Herzegovina declared independence from Yugoslavia on 3 March 1992 and received international recognition the following month on 6 April 1992. This was followed by the Bosnian War. In this war, the Muslims suffered the highest losses in terms of human lives and the economy, relative to the others, because of which thousands of them emigrated and sought refuge in various parts of Europe. 

During that period, the Ahmadiyya Muslim Community assisted these oppressed Muslim refugees as much as possible under the leadership of Hazrat Mirza Tahir Ahmad Khalifatul Masih IV (the), in the spirit of brotherhood. 

The personal guidance of Hazrat Mirza Tahir Ahmad, Khalifatul Masih IV (rh) and the compassion towards the oppressed Muslims was such that, the sincere members of the Community risked their lives and, relying only on God Almighty and obeying the Khilafa they continued visiting Bosnia to offer humanitarian assistance to the oppressed Muslims throughout during this turbulent period. 

Hence, Allah Almighty enabled Jamaat Ahmadiyya to serve the oppressed Muslim Ummah and thus Jamaat Ahmadiyya was established in this country.

After the war, on 28 September 1995, the Central Murabbi, Waseem Ahmed Saro'a, visited the region to continue the welfare work of the Community and the mission officially started in a rented house in Gracanica. The Community's mission was later transferred from Gracanica to Sarajevo, the capital city. 

Allah Almighty enabled the Jamaat to build its own mission house in 2002. And in the year 2003, on the occasion of Eid-ul-Fitr prayers, the Community's mission house 'Masjid Bait-ul-Islam' was formally inaugurated. The Jamaat Ahmadiyya has had the distinction from its inception in Bosnia for its selfless services to the oppressed people throughout the country.