The Graduate Programs of Hawassa University in the areas of agricultural sciences were launched in 2004. At Wondo Genet campus, a joint MSc program, in coordination with the Swedish University of Agricultural Sciences, has been offered since 1996. In 2007, new graduate programs were launched in the areas of Natural Sciences.

The MSc programs aim at producing high-level trained manpower to contribute to the country's research and development endeavors in the different fields of natural and social sciences. Applicants who have a BSc or BA degree in a relevant field of study from a recognized university, are eligible for admission as far as they pass the entrance examinations given for each program. The location of Hawassa, i.e. its proximity to the capital city, Addis Ababa, and most of the national and international research organizations, its presence in the midst of the Rift Valley resort areas which are known for their cultural and biological diversity, makes it a very attractive place to pursue graduate study programs.

At present, there are a total of 30 different MSc programs in the areas of Agricultural Sciences, Natural Sciences, as well as Forestry and Natural Resources Management. The MSc courses are offered in regular programs, Kiremt (Summer) and week-end programs. Currently, about 300 students are enrolled in the different MSc programs of the university. In the near future new programs will be launched in the areas of Social Sciences, Technology and other disciplines. The university, in collaboration with foreign universities, is also planning to launch PhD programs in selected disciplines.

The university has competent senior academic staff for instruction of graduate courses and supervision of thesis research studies. There are also modest computer, library, internet and laboratory facilities for students. Moreover, there are different research projects in the university that offer financial assistance to MSc thesis research on competitive basis. These projects include, CIDA/UPCD project financed by the Canadian International Development Agency, NORAD and NUFU Projects supported by the Norwegian government and the University of Life Sciences of Norway, Rhizobia-Legume Project, and DIF (Development Innovation Fund) of the World Bank. The DIF fellowship is particularly focused to female students, while other projects also give priority to female applicants.

The different MSc Specializations of the university and the departments offering them are listed below.