The excessive use of online gaming before sleep in adolescents could be a risk factor of sleep disorders such as insomnia. This study aimed to assess the association between playing online games before sleep and insomnia based on gender perspective among middle school students in Indonesia. This was a retrospective study and the data came from a cross-sectional survey that included 315 of Grade 8 and 9 students from four middle schools in Jakarta, Indonesia. Self-reported data were collected via a structured questionnaire, which consisted of demographic variables, sleep duration per day, frequency of playing online games before sleep and the Insomnia Severity Index (ISI). Insomnia status was classified into “none or mild” and “moderate to severe” according to ISI score. The proportions of male and female students who often or always played online games before sleep were 50.3% and 21.7%, respectively. Grade 9 students were more likely to have moderate to severe insomnia than Grade 8 students for males (odds ratio—OR = 4.34, p = 0.005) but not for females (OR = 0.69, p = 0.363). However, female students who often or always played online games before sleep were more likely to have moderate to severe insomnia (OR = 4.60, p = 0.001); such an association was relatively smaller for male students (OR = 3.09, p = 0.061). Gender differences should be taken into account when developing health education or interventions.