In 2001, the government issued the policy on organization downsizing that by a decree of the Minister Menkes-Kessos No.: 298/Menkes-Kessos/SK/IV/2001 on April 16, 2001, the six health academies in Yogyakarta were merged into one Politeknik Kesehatan named Politeknik Kesehatan Departemen Kesehatan Yogyakarta, or abbreviated Poltekkes Depkes Yogyakarta. The position of this academy in Politeknik Kesehatan is a department, thus Politeknik Kesehatan Depkes Yogyakarta has 6 departments: Health Analyst Department, (2) Nutrition Department, (3) Midwifery Department, (4) Nursing Department, (5) Dental Nursing Department, and (6) Environmental Health Department. Each department has study programs of Diploma III, Diploma IV, and Applied Bachelor.
As the nomenclature of Department changed into Ministry in 2010, Politeknik Kesehatan Depkes Yogyakarta changed its name to Politeknik Kesehatan Kemenkes Yogyakarta, or abbreviated as Poltekkes Kemenkes Yogyakarta or POLKESYO. In order to improve service performance in all fields, Poltekkes Kemenkes Yogyakarta implements the Financial Management of Public Service Agency (PK-BLU). Financial management of BLU at Poltekkes Kemenkes Yogyakarta is based on the Decree of the Minister of Finance of the Republic of Indonesia No.: 417/KMK.05/2011 dated on December 12, 2011, concerning on the Establishment of Politeknik Kesehatan Yogyakarta at Health Ministry as Government Institution that implements the pattern of Financial Management Public Service Agency. Starting from January 2012, Poltekkes Kemenkes Yogyakarta has been authorized to manage the budgeting independently. With the financial management of BLU, Poltekkes Kemenkes Yogyakarta is expected to provide better education services/p>
In 2012, the Academic Guidance was delegated under the Ministry of Education and Culture RI through the Decree of the Ministry of Education and Culture No. 355/E/O/2012 on October 10, 2012, concerning the Transfer of Study Programs Implementation at Poltekkes Kemenkes RI from Kemenkes RI to Kemendikbud RI. In accordance with the developments, currently, department at Poltekkes Kemenkes Yogyakarta has Professional Education Programs in addition to previously existing programs: Diploma III, Diploma IV, and Applied Bachelors Programs.
In 2019, based on the Decree of the Minister of Research, Technology, and Higher Education (Kemenristekdikti) RI No. 597/KPT/I/2019 on July 18, 2019 regarding the change in study program naming at Politeknik Kesehatan Yogyakarta in Sleman Regency organized by the Health Ministry and the Decree of Kemenristekdikti No. 718/KPT/I/2019 on August 19, 2019 regarding the naming change of Environmental Health Diploma IV Program into Environmental Sanitation Applied Bachelor Program at Politeknik Kesehatan Yogyakarta in Sleman Regency organized by Health Ministry.
Poltekkes Kemenkes Yogyakarta made efforts to develop scientific knowledge through the development of new study programs so that in 2020, POLKESYO obtained a new approval for the health information medical records (RMIK) study program.