Many previous studies have examined metacognitive strategy use among ESL students in offline reading settings, but very few have linked them to a gender context, especially among EFL students when reading online English texts. This research, therefore, explored gender differences in metacognitive strategy usage among Indonesian EFL students in relation to online reading abilities and English proficiency. It enlisted the participation of 426 female and 176 male students from the University of Borneo Tarakan. The data was collected using the OSORS (Online Survey of Reading Strategies), a self-rated online reading ability question, and an English proficiency test. An independent sample t-test, Pearson correlation, and simple and multiple linear regression were used to analyze the data. Significant gender differences were discovered in overall, problem-solving, and support strategy usage, despite the small effect size values, with the female students scoring better on average than the males. For self-assessed online reading ability and online English proficiency, no gender difference was identified. Among the less skilled readers, significant gender differences were identified in overall and support strategies, whereas among the skilled readers, no significant gender differences were observed in both overall and category strategies. There were no gender differences in online English proficiency among the less skilled and skilled readers. Overall strategy use among the females predicted online reading abilities and online English proficiency, while among the males only predicted online reading abilities. These findings add to the growing body of research demonstrating female dominance in EFL online reading programs and have pedagogical implications.