The Faculty of Health Sciences (FIKES) of UIN Syarif Hidayatullah Jakarta is one of the faculties resulting from the expansion of the Faculty of Medicine and Health Sciences (FKIK). FKIK was established on March 12, 2004 with four study programs, namely Pharmacy Study Program (PSF), Public Health Study Program (PSKM), Nursing Science Study Program (PSIK) and Medical Education Study Program (PSPD). PSF and PSKM were officially established with an operating license from the Director General of Higher Education No.1387/D2.2/2004 and No.1338/D/T/2004. PSIK and PSPD operated after the issuance of the decree of the Director General of Higher Education No. 1356/D/T/2005.

In 2011, the study program at FKIK increased with the issuance of an operational permit for the Professional Nurses Study Program (PSPN) from the Director General of Higher Education no 1783/E/T/2011. Then, in 2015 one more study program was added, namely the Pharmacist Professional Study Program (PSPA) after obtaining permission from the Ministry of Research, Technology and Higher Education No.1132/A4/HK/2015.

Along with the development of each study program, based on the Decree of the Chancellor of UIN Syarif Hidayatullah Jakarta No. 141a of 2018 dated 26 February 2018, FKIK was closed and developed into the Faculty of Health Sciences and the Faculty of Medicine. On the same date, the Chancellor appointed Prof. Dr. Arif Sumantri, SKM., M.Kes as Dean of FIKES. Then on April 12 2018, the Chancellor issued Decree No. 248 of 2018 which determines the Head of Study Program (Kaprodi) and Secretary of Study Program (Sekprodi) at FIKES. Since then, the FIKES organization has become complete with 5 existing study programs  namely PSF, PSKM, PSIK, PSPN and PSPA.

Pharmacy and Public Health is a Strata 1 study program which was last accredited in 2018 with an accreditation grade of B, while Nursing Science was accredited in 2019 and has received an A accreditation. Pharmacist is a professional study program which is also accredited B and the Nursing Profession which was accredited in 2019 has received accreditation A. As an institution under the Ministry of Religion which is relatively new, and the accreditation process is at the Mandiri PT Health Accreditation Institute (LAMPT-Kes), the accreditation grades A and B obtained are very good achievements. This shows that FIKES is on par with health education institutions at other large universities. Thus, 40% of study programs at FIKES have been accredited A in 2019.