After the event of 27 April 1978, the Women's General Council was formed as a social-political organization, which was led by Dr. Anahita Ratebzad; this organization was supported by the government. Women's Central Association, which had 360 members, became a second division of this council. Women's General Council had social and political activities among women. This council established its branches in the capital and provinces. The ladies who were leading Women's General Council were: Feroza Marjan, Masooma Esmati Wadak, Soraya, Belqis Tabesh, Jamila Nahid, Guljan, Shahla Sherzad, Tahera Dardmal and Fawzia Nekzad. The activities of Women's Association were mostly vocational training such as cloth sewing, carpet weaving, typing, flower making, beauty parlor, internal decoration, needlework, etc, which were limited to Kabul city.

In 1991 when Mujahedin came to power in Kabul, the Women's Grand Organization was restored, and first led by Mahbooba Hoquqmal and then by Qudria Yazdanparast.

In 1994, parallel to Women's General Organization, Ministry of Labor and Social Affairs restored Women's Association in its organizational structure, which continued its activities until October 1996.

In October 1996 Taliban entered Kabul, and women and girls were forbidden to go to school or work. Taliban incorporated Women's Grand Organization with Women's Association, and hired men instead of women. Taliban regime fell down in 2001. Ministry of Women's Affairs was established according to agreements of Bonn Conference and became part of the executive of the Interim Administration. The male and female employees of Women's Grand Organization and Women's Association were recruited and re-employed. MoWA transformed its strategy from charity activities to policy making.

The first minister of Women's Affairs was Sima Samar who served in this post from 2001 to early 2003. Dr. Habiba Surabi from 2003 to 2004 and Dr. Massoda Jalal from October 2004 to July 2006 served as Ministers of Women's Affairs respectively. In July 2006, Dr. Husn Banu Ghazanfar received vote of confidence from the Parliament to become Minister of Women's Affairs. The ladies who served as deputy ministers in policy and vocational affairs were Shafiqa Yarqin, Soraya Sobhran, Mazari Safa, and deputy ministers in financial and administrative affairs were Tajwar Kakar, Najiba Sharif and Maliha Sahak.

This Ministry has 9 central department and 34 provincial departments.

The first procedural regulation of MoWA as a central institution was passed by decision No. 3 of 05.04.2004 of Ministers' Council, and approved by Decree No. 26 of 24.05.2004 of President of Transitional Islamic State of Afghanistan in 4 chapters and 24 articles. Article three of this regulation states that: MoWA has the responsibility over implementation of political and social policy of the government in order to secure and expand legal rights of women and ensure the rule of law in their lives within its activity area.

Article four:

MoWA, in executing its activities, shall follow the laws, decrees, decisions of Ministers' Council and provisions of this regulation, and ensure its proper implementation in the respective activity areas of this ministry.