Born in British India, Mustafa moved to Pakistan with her family after Partition. She is married and has two daughters.
Mustafa joined Dawn, Pakistan's leading English language daily in 1975 as assistant editor. She was the only woman in Dawn at a senior level who was the first woman leader writer in the mainstream media in Pakistan. During that time she used her gender to her advantage and covered the stories that the men could not cover, such as women's issues concerning health and human rights. She used her perspective as a woman to write editorials promoting international peace and pleading for social justice.
As a female journalist, Mustafa has stated that the injustices Pakistani women suffer "touches her deeply." According to a 2012 Newsline Magazine profile, she mentions how important it is for women to seize the opportunities given to them. Though women's issues was her main beat, she also focused on education, empowerment, health and population. She has stated that focusing on education was important since the root of problems in Pakistan was the country's failure to educate their citizens, especially in health issues.
In 1986, Mustafa was awarded the Global Media Award for Excellence by The Population Institute in Washington for her research and writings on population control in Pakistan. 
In 2012, Mustafa was awarded a Lifetime Achievement Award by the International Women Media Foundation for her coverage on women's issues, politics, educations, health and culture. 
- Global Media Award for Excellence (1986 and 2004) by The Population Institute 
- Pakistan Publishers and Booksellers Association (2005) for her contribution in Books & Authors 
- Lifetime Achievement Award (2012) by International Women Media Foundation (IWMF)
- Zubeida Mustafa, Pakistan 2012 Lifetime Achievement Award International Women Media Foundation (IWMF) Retrieved 18 August 2012.
- Zubeida Mustafa, Profile Newsline. Retrieved 18 August 2012