This study's objectives were to investigate and analyze comparisons of students' learning motivation during online learning based on gender. This quantitative study used a survey design. The subject study consisted of 331 students in the high school selected from science majors using the convenience sampling technique. The Instrument was adopted by The Motivated Strategies Learning Questionnaire (MSLQ), which consisted of five aspects (self-efficacy, intrinsic value, test anxiety, strategy use, self-regulation). The Instrument was tested valid and reliable to use. Data analyzed was used descriptive statistics and Mann Whitney test. These findings that the female student's mean score of learning motivation is higher than the male student's mean score. Based on the Mann-Whitney test results, there is a significant difference in the mean score of learning motivation between male and female students. Finally, we suggest further research on gender differences in learning motivation using a larger population and more extensive research about investigating the relationship or influence of students' learning motivation toward gender.