Atma Jaya Catholic University of Indonesia consists of eight (8) faculties and twenty one (21) study programs for graduate program (S1). These eight faculties are including: Faculty of Economics and Business (FEB), Faculty of Business Administration and Communication Studies (FIABIKOM), Faculty of Education and Languages (FPB), Faculty of Engineering (FT), Faculty of Law (FH), School of Medicine and Health Science (FKIK), Faculty of Psychology (FP), Faculty of Biotechnology (FTb)

Atma Jaya Catholic University of Indonesia also offers its graduate programs, one of which is Master Program (S2). The Master Program of Atma Jaya Catholic University of Indonesia include Master of Management (MM), Master of Applied English Linguistics, Master of Professional Psychology, Master of Biotechnology, Master of Science of Psychology, Master of Law, and Master of Mechanical Engineering.

Besides the Master Program, Atma Jaya Catholic University of Indonesia offers its Doctoral programs, including Doctor of Applied English Linguistics and Doctor of Psychology.

Atma Jaya Catholic University of Indonesia provides opportunities for special training to students who intend to prepare themselves before entering the workplace through its professional programs. One professional program offered by Atma Jaya Catholic University of Indonesia is the Professional Program in Accounting (PPAk).