Health Services Academy was established in 1988 as a department of the Ministry of Health, Government of Pakistan, and provided short courses and training for public health professionals. Since its humble beginnings as a training institute, the Academy has grown steadily and has established itself as the premier institute of public health in Pakistan, looking to provide more academic programmes in the near future, as well as providing an environment that focuses on excellence in academics, research, and policy-making.

With assistance from the German Technical Cooperation (GTZ), HSA began to offer a Master's in Public Health (MPH) degree in 1995, and the first batch of students graduated in 1996. The initial curriculum was designed by Dr. Arnfried A. Kielmann and Dr. Sameen Siddiqi. During the past ten years, eight cohorts of alumni have graduated from the institution with a Master's in Public Health (MPH), and these alumni are now engaged in a wide range of exciting endeavours across Pakistan in both the public and private sector. The Academy remains the most applied to school of public health in Pakistan, and is established and well on its way to achieving its institutional objectives.

Since all leading academic and research organizations require autonomous status in order to create an environment of academic excellence, the Ministry of Health promulgated an ordinance entitle Health Services Academy Ordinance, 2002 , put into place in November, 2002. Following the implementation of this ordinance from July 1, 2003, the Board of Governors has been supervising the overall affairs of the Academy.

Recently, HSA has moved to a new campus in Chak Shahzad, revised its MPH programme to a two-year MSPH programme, and is in the process of overhauling all its IT infrastructure, its library, and its academic rules and regulations. Under the new leadership of Dr. Shakila Zaman, Director HSA, and Dr. Paul Rueckert, Principle Advisor to HSA, GTZ, it is hoped that HSA will produce well-trained and competent public health professionals, and thus improve health care delivery in Pakistan.