The cost of education in the undergraduate program (S1) at UIN Sunan Kalijaga Yogyakarta applies a Single Tuition System (UKT) which is determined based on the economic ability group of prospective students and must be paid at the beginning of each semester. Prospective students of UIN Sunan Kalijaga Yogyakarta from the SNBP, UTBK-SNBT, SPAN-PTKIN, UM-PTKIN and Independent Pathways are grouped into one of the UKT groups.
 
Registration fees and tuition fees that have been paid cannot be withdrawn for any reason.
 
Decree of the Minister of Religious Affairs of the Republic of Indonesia Number 498 of 2024 concerning Single Tuition at PTKIN in the Ministry of Religious Affairs for the Academic Year 2024 - 2025.