Medical students are often considered a high-risk group for stress-related conditions, including primary headaches. Previous research on primary headaches in this population has shown an association between poor academic performance and the need for intervention. This study aimed to assess the prevalence of primary headaches among medical students at Northern Border University in Arar, Saudi Arabia. This cross-sectional study used an online questionnaire administered at a single point in time. The study sample included 405 medical students from Saudi Arabia, of whom 50.9% were males, 49.1% were females, and 91.9% of participants were aged 18-24 years. The frequency of headache attacks was reported as once daily by 54.2%, twice daily by 18.7%, and three times daily by 17.6%, while 33 participants experienced one headache attack weekly, 23.5% had 2 attacks weekly, and 25.6% had three attacks weekly. In terms of intensity, 34.5% reported severe headaches, 34.8% moderate headache, and 30.7% mild headache. Headaches were often accompanied by symptoms such as nausea (46%), vomiting (42.7%), photophobia (56.5%), phonophobia (60.9%), and neurological disturbances (48.3%). Approximately 29.7% of participants used prescribed headache medications, while 18.9% self-medicated without a prescription. Primary headache is highly common among medical students in Saudi Arabia, posing a significant challenge to their quality of life and academic performance. It is essential to emphasize the importance of consulting a neurologist if headaches are experienced.