Background: The pandemic of COVID-19 has resulted in multiple precautions to control the infection, one of which is transforming students’ schools into virtual classrooms. These new situations may pose additional challenges for some individuals such as epilepsy patients who account for 5.5% of school children (6–18 years). This study aimed to determine the effect of virtual learning on seizure control among epilepsy patients. Methods: This is an online-based cross-sectional study that was performed between 17 February to 27 June 2021 among patients with epilepsy who attend virtual learning classes. The questionnaire was distributed to the patients at a single-center neurology clinic in Mecca, Saudi Arabia. We included all patients who were diagnosed with epilepsy at any hospital, aged between 10 to 30 years, and living in Saudi Arabia. Results: A total number of 70 patients were included in the study. Patients’ gender was nearly equally distributed between the two groups with females predominant (51%). The average time of more than 10 hours spent on screens and electronic devices was remarkably increased during COVID-19 (20.0% to 45.7%). The average number of seizures per year has a double-fold increase during the pandemic for ≥7 attacks (increased from 10% to 20%). More than half of the patients had a significant increase in their seizure frequencies during virtual learning (60%). Patients with focal epilepsy, a history of photosensitivity, and patients with disturbed sleep patterns are significant risk factors associated with increased seizure frequencies during virtual learning. Conclusions: Focal epilepsy, history of photosensitivity, and disturbed sleep pattern associated with increased seizure frequencies during virtual learning. Time spent on screen has no significant relation to increasing seizure frequencies. Identifying the patients’ risk and taking a serious step in reducing its sources is important in order to provide a better quality of life.