Given the perceived imbalance in resource allocation and the recognized disparities in degree completion rates across academic disciplines in Japan's higher education system, this study explores the perceptions and experiences of graduate students through a comparison between graduate students in Humanities and Social Sciences and those in Sciences and Engineering. Osaka University has been chosen as the case study because it is one of the former empirical and research-intensive universities located in the international city of Osaka, Japan, which is well-known as one of the most DEI-promoting universities in Japan. The data from the Students Experiences in the Research University (SERU) survey conducted at Osaka University from 16th November 2020 to 19th February 2021 was utilized in the study to delve into graduate students' perceptions of their host institutions and their individual issues. The study suggests that graduate students in Sciences and Engineering generally had better learning and research experience at both institutional and individual levels, including a higher level of recognition and satisfaction with academic context (e.g., advising, guidance, facilities, and opportunities) and financial support (e.g., scholarships and research assistantships). Regarding the organizational climate, the data analysis reveals that graduate students in Humanities and Social Sciences tend to depict their institutions as a more accommodating and welcoming environment for students with diverse backgrounds. At an individual level, overwhelmingly graduate students in Humanities and Social Sciences considered themselves less competent regarding their professional knowledge and skills, which leads to significant anxiety and concern about their future employment. Based on the research findings, several recommendations are offered to both researchers and university administrators to address the identified issues and provide enhanced support for students in the future.