Problem-based learning (PBL) is a constructivist approach to learning which is believed to promote reflective thinking in students. This study investigated how students in one particular institution developed in their reflective thinking habits—Habitual Action, Understanding, Reflection, and Critical Reflection—as they went through the daily practice of PBL. A 16-item questionnaire measuring the four levels of reflective thinking habits was administered to four cohorts of students: an incoming cohort, first-years, second-years, and third-years. First-year students rated themselves higher on Reflection and Critical Reflection, while third-years reported the highest levels of Habitual Action. Discriminatory and scatterplot analysis on the third year cohort revealed that while a proportion of students (47%) reported higher levels of Habitual Action with lower levels of Reflection, there was a small subgroup who also reported higher levels of both Habitual Action and Reflection. Overall, the results showed that PBL does promote the development of reflective thinking, particularly for first-year students, but that this development is not sustained consistently after that. This pointed to other possible factors that could hinder students’ development of reflective thinking in PBL.