Boko Haram is a militant organization who has purpose to declare an Islamic State in Nigeria. Boko Haram was established on 2002 in Maiduguri under a leadership of Muhammad Yusuf. On 2009, Muhammad Yusuf died and replaced by Abu Bakar Shekau on 2010. In effort to eradicate Boko Haram, Nigerian Government has formed JTF (Joint Task Force) to ensure the peace, order, and stability in Nigeria. The conflict between Boko Haram against Nigerian Government has already determined as a non-international armed conflict by International Criminal Court (ICC). Non-international armed conflict is regulated in common article 3 to Geneva Convention 1949. This research will discusses about the protection of civilian population in non-international armed conflicts under The Fourth Geneva Convention 1949 and Additional Protocol II 1977. By using normative legal research, the study describes about the application of International Humanitarian Law. The result shows that the application of International Humanitarian Law was not fully implemented in Nigeria. Both Boko Haram and JTF have violated the Geneva Convention 1949 and Additional Protocol II 1977. During 2009 to 2017, the hostilities between Boko Haram and Nigeria Government caused the death of 20.000 victims. According to the study of Vision of Humanity, 77% of victims are civilians. International Committee of the Red Cross (ICRC) has an authority to give humanitarian assistance for every party who are involved in the hostilities or armed conflicts based on common article 3 to Geneva Convention 1949.