After becoming a faculty in 1993, although it was still under the structure of the USU Postgraduate School, in 1999 the Undergraduate Public Health Study Program (two) was born through the Decree of the Director General of Higher Education, Ministry of National Education of the Republic of Indonesia No. 295/DIKTI/Kep/1999 dated 16 June 1999 with an interest in Occupational Health studies. In 2000, a new program was born, namely the Health Administration and Policy Study Program (Decree of the Director General of Higher Education, Ministry of National Education of the Republic of Indonesia, No. 353/DIKTI/Kep/2000; September 25, 2000). This study program then develops 5 study interests: 1) Health Administration and Policy, 2) Hospital Administration, 3) Community Health Administration/Epidemiology, 4) Community Nutrition Administration and Policy, and Health Disaster Management.

In 2005, the Decree of the Director General of Higher Education, Ministry of National Education of the Republic of Indonesia, No. 136/D/T/2005 dated 10 May 2005 concerning the Establishment of the Industrial Environmental Health Management Study Program. Subsequently in 2007, all Masters Study Programs whose main body was Public Health Sciences, through USU Chancellor's Decree No 1535/H5.1.R/SK/PRS/2009, were placed in FKM USU. The name of the study program was changed to Study Program (S-2) of Public Health Sciences. The Doctoral Study Program in Public Health Sciences was then opened in 2009 through USU Chancellor's Decree No. 929/H5.1.R/SK/PRS/2009. The three study programs (S1, S2, and S3) currently at FKM USU are currently accredited by BAN PT with a "B" rating until 2020.

Based on USU Chancellor's Decree No. 28/H5.1.R/SK/PRS/2010, Public Health Science Master Study Program opens an Interest in Reproductive Health Studies. Thus since the 2010/2011 academic year, the FKM USU Masters Study Program has 9 Study Interests, namely:

• Health Administration and Policy
• Hospital Administration
• Community Health Administration/Epidemiology
• Public Nutrition Administration and Policy
• Disaster Health Management
• Occupational Health
• Health Promotion and Behavioral Sciences
• Industrial Environmental Health Management
• Reproduction health