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In this study, we analyzed the effect of brain-based science learning. Based on the research results from 2001 to April 2018, we used 827 research articles that can be read in the original text as the primary analysis target when the search terms were ‘brain based learning science’, ‘brain based education science’ and ‘brain based learning science’. Then, we set PICOS (population, intervention, comparison, outcome, study design) which is the criterion for selecting the final analysis target. Based on PICOS, 27 research articles were selected as the final analysis target. A total of 81 effect sizes were calculated from 27 research articles. To reduce the threat of internal validity when calculating multiple effect sizes in the same research article, meta-analysis was conducted using ‘shifting unit of analysis’. In this study, the effect size was calculated by the Hedge’s g, which represents the standardized mean difference. The main results of this study are as follows. First, the effect of brain-based science learning are moderate(g=0.78, U3=78.23). When analyzed by dependent variables, there was no statistically significant difference in the average effect size between dependent variables. However, when science knowledge was used as a dependent variable, the effect size of the research tended to be the largest(g=0.59, U3=72.24), Second, as a result of the meta-ANOVA, there was a statistically significant difference in the average effect size between experimental designs (Q=4.50, df=1, p<0.05). The average effect size value obtained from a single group pre-post test design was greater than value of others. Third, the average effect size values vary statistically significantly depending on whether the target audience for gifted children(Q=7.866, df=1, p<0.05). The brain-based science learning for gifted students was more effective. Fourth, the average effect size values by publication type showed no statistically significant differences(Q=5.14, df=2, p>0.05). Based on the findings, the research will discuss ways and directions to effectively improve brain-based science learning.