The purpose of this study was to identify the relationship among critical thinking skill, gender and motivation in 9th grade students of Junior High School in Kuningan. This descriptive study used purposive sampling that comprised 110 ninth grade students taken from three junior high school that has good computer literacy and use 2013 curriculum. The data were obtained through Science Virtual Test on living things and environmental sustainability theme, respondent identity, and science motivation questionnaire (SMQ). Female students scored highest on generating purpose skill (M = 73.81), while male students performed better on generating implication and consequences skill (M = 78.01) where both groups differed significantly (p = 0.011). Students scored highest on generating purpose skill for high and moderate motivation group, while for the lowest score, moderate and low motivation group performed it on making assumption skill. Additionally, some critical thinking elements differed significantly by motivation to learn science. Despite, there was no correlation between students’ critical thinking and motivation (r = 0.155, p > 0.05). The finding indicated that students’ critical thinking is not differed by gender and not affected by motivation to learn science.