Cognitive enhancement, a technical intervention aimed at enhancing human cognitive abilities such as learning and memory, is primarily discussed in relation to its educational purposes. Particularly, cases of misuse of methylphenidate for cognitive enhancement purposes have been consistently reported not only in the United States but also among students in South Korea, prompting a need for discussions on the appropriateness of such cognitive enhancer use. Therefore, in this study, we aimed to examine the issue of cognitive enhancement more specifically in relation to its use for educational purposes, and whether the cognitive changes induced by methylphenidate contribute to the thinking skills aimed at education. Previous studies have found that the activation of specific brain activities due to cognitive enhancement, including methylphenidate, leads to the deterioration of other aspects of function, and that while it generally helps with cognitive stability, it inhibits cognitive flexibility. To explore whether such cognitive changes can contribute to enhancing the thinking skills pursued by education, this study explored discussions on thinking skills by John Dewey and Matthew Lipman. Consequently, contrary to proponents of cognitive enhancement, we find that the continuous use of cognitive enhancers may have a negative impact on the development of thinking skills. As an alternative, appling Thea Ionescu’s cognitive pattern of variability-stability-flexibility, we suggest that temporary use at the stage transitioning from variability to stability, rather than continuous use of cognitive enhancer, may have a positive impact on educational purposes. At a time when cognitive enhancement technologies are advancing, this study argues that we need more specific discussion on what is appropriate cognitive enhancement in education.