Clinical reasoning competency is essential for an appropriate clinical dental treatment. Among the tools for the assessment of clinical reasoning competency, computer-based testing (CBT) is considered more useful than paper-based testing (PBT), because teachers can control the timing of information given to the examinees. Such timings could possibly affect the thinking process of examinees. However, few studies reported differences of reasoning between the two testing modes. In the present study, we developed an assessment of clinical reasoning and applied it using CBT and PBT to compare the examinees' performance. The participants comprised 60 students in the fifth-year class in 2012 of the School of Dentistry, Faculty of Dentistry, Tokyo Medical and Dental University. The tests comprised 25 problems, each with four questions, totaling 100 questions. The contents of the questions were the same in CBT and PBT. The students were assigned to CBT (Group C, n = 30) and PBT (Group P, n = 30) groups, with an almost equal gender ratio in the groups. The difference between scores was analyzed with a univariate analysis of variance. No significant intergroup differences were found regarding the test duration, total score, and average score of each question. The number of problems with perfect marks was higher in Group P than in Group C (P < 0.05), probably because Group P students could access the information of the previous question (s) within a problem. Thus, the differences of the examinees' performance between the two testing modes were small.