Since schools cannot use face-to-face tests to evaluate students’ learning effectiveness during the COVID-19 pandemic, many schools implement computer-based tests (CBT) for this evaluation. From the perspective of Sustainable Development Goal 4, whether this type of test conversion affects students’ performance in answering questions is an issue worthy of attention. However, studies have not yielded consistent findings on the equivalence of the scores of examinees’ answering performance on computer-based tests (CBT) and paper-and-pencil tests (PPT) when taking the same multiple-choice tests. Some studies have revealed no significant differences, whereas others have exhibited significant differences between the two formats. This study adopted a counterbalanced experimental design to investigate the effects of test format, computerised presentation type, difficulty of item group, and administration order of item groups of different difficulty levels on examinees’ answering performance. In this study, 381 primary school fifth graders in northern Taiwan completed an achievement test on the topic of Structure and Functions of Plants, which is part of the primary school Natural Science course. The achievement test included 16 multiple-choice items. After data collection and analysis, no significant differences in the answering performance of examinees were identified among the PPT, CBT with single-item presentation, and CBT with multiple-item presentation. However, after further analysis, the results indicated that the difficulty of item group and the administration order of item groups of different difficulty levels had significant influences on answering performance. The findings suggest that compared with a PPT, examinees exhibit better answering performance when taking multiple-choice tests in a CBT with multiple-item presentation.