Effective resource planning in higher education requires anticipating student demand for courses, especially when dealing with elective programs. Monitoring student preference is a recurring topic in the literature; however, to the authors’ knowledge, no simple methods for estimating student preferences when choosing courses in higher education have been proposed. This study develops and explores the use of a simple questionnaire to capture patterns in student course preferences within a university context. The research is developed in the context of the nine Cross-Over modules offered as part of the curriculum of the master’s programs (MSc) of the Faculty of Civil Engineering and Geosciences of Delft University of Technology (The Netherlands). No prior registration is required far in advance for these courses, making an accurate estimation of student numbers critical for the planning and allocation of educational resources. The developed questionnaire is applied three times in two different academic years to the students’ choice of Cross-Over modules. The questionnaire was shared in 2021, with 225 responses out of 339 students, in 2022, with 159 responses out of 365 students, and in 2024, with 94 responses out of 272 students. Student enrollment in the academic year 2023/2024 is used to assess the performance of the questionnaire. The questionnaire is able to capture general preferences of the students, providing fair estimates of the number of students per course; larger differences are observed in courses with a lower number of students. In addition, some patterns were identified in student preferences: there is a relationship between the first and second choices, and students usually choose modules closer to their own disciplines. The developed questionnaire provides with a reasonable first estimation of the expected number of students in courses, allowing for better planning and allocation of educational resources beforehand.