Investigation about metacognitive awareness of reading strategies (MARS) has mainly focused on paper-based reading rather than online reading. Gender, reading media preferences, and English proficiency levels (EPL) account for students’ differences in MARS. However, existing studies are still debating the predictive power of these variables on MARS. MARS was assumed to influence English reading comprehension even though research that firmly supports this assumption seems rare. Therefore, we examined Indonesian university students’ MARS in online reading activities using data from 1412 university students in Indonesia. They were categorized into gender, reading media preferences, and EPL. The One-Way MANOVA results showed students’ differences in MARS based on their gender, (F = 20.456, p < 0.05), reading media preferences, (F = 2.82, p < 0.05), and students’ EPL, (F = 5.988, p < 0.05). The multiple regression analysis showed that global, support, and problem-solving strategies were simultaneously associated with English reading comprehension scores. This study emphasizes the effect of the variables on students’ MARS differences and discloses the association between MARS and English reading comprehension.