The small scale of the GPGS and the diverse specializations, broad experience, and research interests of the faculty enable flexible course selection. In consultation with faculty members, students select courses designed to meet their individual interests and to further the acquisition of specialized knowledge in their chosen fields.

The master's degrees have two tracks; each track has different graduation requirements. Students in the thesis track write a research thesis while those in the credit track comlete a graduation project. The selection of the track takes place after a student matriculates in the program. Those who seek to enter the thesis track need to apply for it, typically at the start of the second semester, with entry contingent upon academic performance, availability of a mentor for the proposed topic, and successful defense of a thesis proposal.

Doctoral students work on their dissertation under the guidance of a advisor. While no course work is required, candidates participate in workshops and other activities and may, in consultation with their dissertation advisor, attend courses.

English is the language of instruction. However, the study of Japanese is encouraged. Students may take adantage of the comprehensive Japanese language courses offered at Sophia. Those with a sufficient level of Japanese language proficiency as determined by a language examination may also take courses taught in Japanese as part of their studies. Additionally, students may study other languages at Sophia that are relevant to their studies, depending on availability of space in the courses.