Klemenčič's research spans several areas within sociology and politics of higher education, and is mostly international comparative and or focused on European higher education.
The study of higher education impact on students has been one of the most prolific subfields in sociology of higher education and explores variety of ways that higher education influences student outcomes. Klemenčič's research seeks to corrects this one sided perspective arguing that student too have impact on their colleges and universities. Klemenčič introduces theory of student agency as students’ capabilities to intervene in and influence their learning pathways and educational environments. She investigates student impact on higher education through student representation, student activism, student voluntary service and student campus employment as students having direct effects on higher educaion. In addition, she investigates indirect effects studnets have on higher education through consumer preferences and consumer behaviour.
Klemenčič has investigated European policies and practices on SCLT both analyzing the theoretical underpinnings of policies and offering prescriptive advice. With Sabine Hoidn she developed the model of student centered learning and teaching ecosystems and theorized student agency and actorhood in student centred learning and teaching.
Klemenčič investigated institutional research in Europe and in Central and Eastern European countries and student involvement in quality assurance.
In research on civic role of universities, Klemenčič has focused mostly on education function preparing students for citizenship and civic engagement. Klemenčič argues that to develop students' civic agency and dispositions for active citizenship and civic involvement two measures are needed. One is to build-in these topics into regular classes and create connections to real-world problems as part of the existing course offer when possible (as opposed to offering special "civics" courses). Another measure is for universities and colleges to operate as sites of citizenship and civic involvement. Through practices of student representation in decision-making and offering opportunities to students for public service on campus, colleges and universities enable student university citizenship. Through representative and service roles, students learn how to enact their civic agency in an institutional context. Any by having opportunities for civic engagment their sense of belonging to the home institution and their sense of ownership of their institution strenghten. Both are important for student wellbeing.
Klemenčič has been a member of the Slovenian research team within the Global Network on Academic Profession in Knowledge Societies (APIKS), which is a continuation of decades long international comparative research on Changing Academic Profession (CAP). Over 20 national teams are conducting system-wide surveys of academic staff based on a common questionnaire. The Slovenian team conducted a system-wide survey in 2013 and 2018 on the conditions of academic work and the state of academic profession. Klemenčič was specifically interested in the questions of academic imbreeding in the Slovenian academic space and academic staff's agency towards internationalisation of higher education.
Klemenčič's most important contribution in this area is on internationalization of higher education in peripheral countries and on academics as agents of internationalization. She developed a framework for integrated international engagements arguing for multiple layers of international cooperation as "gears" that mutually reinforce internationalization efforts. Klemenčič also researched the effects of Erasmus programme on higher education developments, and regional cooperation in higher education.
The gear effects of integrated international engagments (Klemenčič 2015, p. 6)
Klemenčič has researched various aspects of higher education policies and reforms in general, and in Europe, Western Balkans and Slovenia in particular.