Nonterm, direct assessment competency-based education (CBE) represents a significant reimagining of the structure of higher education. By regulating students' progress through the program based on their mastery of tightly defined competencies rather than on the time spent learning them, this learning environment affords students far greater flexibility than traditional programs. This focus on defined competencies has led to concerns that students in these types of programs may not demonstrate higher level skills, such as critical thinking, at levels comparable to those enrolled in more traditional programs. This study evaluated 39 students' demonstration of critical thinking in two assessments administered in parallel versions of one course: one offered through the nonterm, direct assessment CBE University of Wisconsin Flexible Option, and the other offered through a traditional online program. For this study, each of the 78 assessments was scored using the critical thinking rubric from the Valid Assessment of Learning in Undergraduate Education (VALUE) project. We found that students from the CBE version of the course received significantly higher (p = 0.0013) overall scores than the students in the traditional online version of the course. While further research is required to refine these methods and ensure the generalizability of these results, they do not support concerns about students' abilities in this learning environment.