The measurement of computational thinking ability among computer science (CS) university students is of paramount importance. This study introduces UniCTCheck, a novel method designed to assess the main components of computational thinking in CS students. Utilising two key instruments, namely, the web application CTScore and the psychometric scale CTProg, this research aims to precisely evaluate seven core components of computational thinking and six programming concepts skills essential for CS students. The study, conducted at Rey Juan Carlos University and Atlantic Technological University Galway, involved a diverse sample of students from different year levels and programme specialisations. Through a rigorous research design, including sampling strategies and data collection tools, this study seeks to address critical research questions related to the measurement of variations in students’ computational thinking and programming skills by gender, university level, and location. By shedding light on the significance of computational thinking and programming in the educational realm, this research contributes to the existing literature and underscores the essential role of computational skills in the modern era.