This study aimed to develop and validate a comprehensive core competency assessment instrument specifically designed for undergraduate students at a research-focused university. Despite growing emphasis on competency-based education (CBE), there are limited psychometrically sound tools tailored to evaluate students’ level of core competencies in research-intensive universities. The current study proceeded in three phases: (a) development of a conceptual framework comprising six core competencies: Integrated Thinking, Knowledge Inquiry, Creative Integration, Global Citizenship, Communication & Collaboration, and Self-Management; (b) item generation and expert validation; and (c) validation through exploratory and confirmatory factor analyses. The final instrument included 77 items across the six competencies. CFA confirmed adequate model fit (CFI = .934–.957; RMSEA = .057–.088). The results showed that the validated instrument can provide a reliable and comprehensive assessment for students' core competencies in research-oriented university settings. This instrument can provide guidelines for developing competency-based education (CBE) curricula in higher education, as well as criteria for evaluating and refining existing CBE programs. This instrument functions as both a psychometrically robust assessment tool and a practical guide for institutional enhancement. It enables precise measurement of students’ core competencies, offering evidence that can inform curriculum design, academic advising, and policy development. In addition, the validated framework lays a strong groundwork for future research to investigate the long-term effects of competency-based education on student achievement, career readiness, and personal development across various higher education settings.