UNY ensures that all units establish and implement strategic planning (Rencana Strategis/RENSTRA) in accordance with UNY's guidelines. The university's strategic planning is aligned with the university's mission, vision, and core values and follows the Ministry of Research, Technology, and Higher Education's strategic planning (Regulation of Ministry of Research, Technology, and Higher Education No 50 Year 2017; Regulation of Ministry of Education and Culture No. 22 Year 2020). Every five years, the planning is regulated, so 2020-2025 RENSTRA (Rector Regulation No. 12 Year 2020) is now in effect.

The study programmes are crucial in achieving the strategic goals, which are measured using a set of key indicators. Ten strategic aims encompassing the pillars of higher education are part of the strategic planning (education, research, and community service). The institution establishes four strategic policies with the goals of (1) improving educational quality, (2) fostering creativity and innovation, (3) enhancing student competitiveness, and (4) enhancing academic prestige. As a result, ten strategic targets have been set to guide the four strategic policies' implementation. UNY itself is regularly accredited by the national accreditation bureau of higher education (known as BAN-PT). This accreditation is focused on the eighth standards of higher education. After desk evaluation and site visit, UNY was accredited A by BAN-PT as stated in the SK 3127/SK/BAN-PT/Akred/PT/XII/2016. As per 2020, the criteria for the accreditation have changed from A, B, C to Unggul, Very Good, and Good.