TIMSS 1999, 2003, 2007 and PISA 2006 data were used to investigate gender differences in the science performance. Each student was assigned to one of quartile group based on his science performance. For each group, gender differences in central tendency, standard deviation, and numbers were examined. The results indicate that gender differences are generally small. However, the scores of male consistently have larger variances. Most of gender differences in mean, standard deviation ratio, and ratio of the male numbers to the female numbers from groups below Q1 and above Q3 are significant. Female outperforms male in group below Q1, while male outperforms female among high-scoring group. In those two groups, the scores of male have larger variance. Males outnumber females substantially among high performing group. The results of gender difference pattern from TIMSS and PISA are inconsistent. The gender gap is slightly larger in grade 8 than in grade 4. It is suggested that sample be well specified in terms of ability levels and gender differences be examined by multiple statistical indicators