- Bachelor of Arts in Creative Writing
- Bachelor of Arts in English Language
  - Track 1 : English Language Studies
  - Track 2 : English across the Professions
- Bachelor of Arts in Filipino
- Bachelor of Arts in History
- Bachelor of Arts in Literary and Cultural Studies
- Bachelor of Arts in Philosophy
- Bachelor of Arts in Political Science
- Bachelor of Arts in Anthropology
- Bachelor of Arts in Literature Across the Professions
- Bachelor of Arts in Sociology
- Bachelor of Science in Biology
- Bachelor of Science in Chemistry with Certificate in Chemical Technology
- Bachelor of Science in Geology
- Bachelor of Science in Mathematics
- Bachelor of Science in Pharmacy
- Bachelor of Science in Physics
- Bachelor of Science in Psychology
- Bachelor of Science in Social Work

College of Business Administration

- Bachelor of Science in Accountancy
- Bachelor of Science in Business Administration, with Majors in Business Analytics, Economics, Financial Management, Human Resource Management, Operations Management and Marketing Management
- Bachelor of Science in Entrepreneurship
- Bachelor of Science in Office Systems Administration

College of Computer Studies

- Bachelor of Library and Information Science
- Bachelor of Science in Computer Science
- Bachelor of Science in Information Systems
- Bachelor of Science in Information Technology

College of Education

- Bachelor of Elementary Education
- Bachelor of Early Childhood Education
- Bachelor of Special Needs Education
- Bachelor of Science in Nutrition and Dietetics
- Bachelor of Secondary Education, Major in English
- Bachelor of Secondary Education, Major in Filipino
- Bachelor of Secondary Education, Major in Values Education
- Bachelor of Secondary Education, Major in Mathematics
- Bachelor of Physical Education
- Bachelor of Secondary Education, Major in Science
- Bachelor of Secondary Education, Major in Social Studies

College of Engineering and Design

- Bachelor of Science in Architecture
- Bachelor of Science Civil Engineering
- Bachelor of Science in Computer Engineering
- Bachelor of Science in Electrical Engineering
- Bachelor of Science in Mechanical Engineering

College of Mass Communication

- Bachelor of Mass Communication
- Bachelor of Mass Communication, Major in Broadcasting

College of Nursing

- Bachelor of Science in Nursing

College of Performing and Visual Arts

- Bachelor of Fine Arts in Studio Arts
- Bachelor of Music in Music Composition
- Bachelor of Music in Music Education
- Bachelor of Music in Music Performance with Majors in Piano, Voice and Choral Conducting
- Bachelor of Performing Arts, Major in Speech and Theater
- Bachelor of Music, Major in Music Therapy

Institute of Clinical Laboratory Sciences

- Bachelor of Science in Medical Technology
- Institute of Rehabilitative Sciences
- Bachelor of Science in Physical Therapy

Institute of Environmental and Marine Sciences

- Bachelor of Science in Marine Biology

Divinity School

- Bachelor of Liturgy and Church Music
- Bachelor of Theology, Major in Pastoral Ministry

School of Public Affairs and Governance

- Bachelor of Science in Foreign Affairs
- Bachelor of Science in Public Administration

College of Law

- Juris Doctor

School of Medicine

- Doctor of Medicine

Graduate and Postgraduate Degrees

College of Agriculture

- Master of Applied Science in Systems Agriculture

College of Arts and Sciences

- Master of Arts with Majors in Anthropology, Sociology, Extension Administration, Filipino, History
- Master of Arts in English with Concentrations in English Language Studies, Teaching English to Speakers of Other Languages, Literary Studies, Creative Writing
- Master of Arts in Philosophy
- Master of Arts in Psychology with Majors in Counseling Psychology, Industrial/Organizational Psychology, Social and Community Psychology, Sports and Exercise Psychology
- Master of Science in Biology, Mathematics, Physics, Social Work
- Doctor of Philosophy in English
- Doctor of Philosophy in Psychology with Majors in Clinical Psychology and Social-Organizational Psychology

College of Business Administration

- Master of Business Administration

College of Computer Studies

- Master of Information Systems

College of Education

- Master of Arts in Education with Majors in Educational Management, Guidance and Counseling, Educational Technology
- Doctor of Education
- Doctor of Philosophy in Education with Majors in Administration and Research and Evaluation

College of Engineering and Design

- Master of Engineering with Majors in Civil Engineering, Computer Engineering, Electrical Engineering, Mechanical Engineering

College of Nursing

- Master of Science in Nursing with Majors in Adult Health, Community Health Nursing, Family Nursing Practice, Nursing Administration, Psychiatric Mental Health Nursing
- Doctor of Philosophy in Nursing

College of Performing and Visual Arts

- Master of Music with Majors in Choral Conducting, Instrumental Conducting, Ethnomusicology, Music Education

Institute of Environmental and Marine Sciences

- Master of Science in Marine Biology
- Silliman University – Newcastle University Double Degree Program: [Master of Research in Marine Ecosystems and Governance (Newcastle University) and Master of Research in Tropical
- Biological Oceanography (Silliman University)]
- Doctor of Philosophy in Marine Biology

School of Public Affairs and Governance

- Master of Public Administration specializing in Fiscal Administration, specializing in Local Administration
- Master of Public Health with Concentrations inHealth Education, Environmental Health, Public Health Administration, Public Health Sociology
- Doctor of Public Administration
- Doctor of Philosophy in Public Administration
- Doctor of Philosophy in Social Science

Divinity School

- Master of Divinity with Majors in Biblical Studies, Christian Education, Pastoral Ministry, Mission Studies, Spiritual Care/CPE, Systematic Theology
- Master of Peace Studies
- Doctor of Theology in Christian Education
- Doctor of Theology Major in Christian Ethics
- Doctor of Theology Major in Biblical Studies
- Doctor of Theology Major in Systematic Theology

Associate and Certificate Programs

Arts and Sciences

- Certificate in Chemical Technology
- Certificate in Southeast Asian Studies
- Certificate in Philippine Studies
- Certificate in Teaching Philosophy
- Certificate in Disaster & Psychosocial Management
- Certificate in Gender Studies
- Certificate in Health Psychology
- Certificate in Personnel Psychology
- Certificate in Psychology
- Certificate in Sports and Exercise Psychology
- Certificate in Teaching English to Speakers of Other Languages
- Certificate in Poetry Writing
- Certificate in Short Fiction Writing
- Certificate in Playwriting
- Certificate in Critical Writing

Environmental and Marine Sciences

- Certificate in Coastal Resource Management

Divinity School

- Associate in Liturgy and Church Music
- Certificate in Church Music
- Certificate in Liturgy
- Certificate in Clinical Pastoral Education

Education

- Certificate in Professional Education

Mass Communication

- Certificate in Environmental Journalism

Performing and Visual Arts

- Associate in Music Programs in Choral Conducting, Music Theater, Opera, Bandurria, Octavina, Laud
- Advance Certificate in Music Specializing in Music Technology, Dance, Guitar, Piano, Voice, Cornet, Clarinet, Baritone, Flute, Tuba/Sousaphone, Saxophone, Trumpet, Trombone, French Horn, Choral Conducting, Sacred Music, Theater Design & Stage Craft, Play Production, Speech Improvement