Background <p>Headache disorders are among the most common neurological conditions globally, yet their impact on university students, particularly in low and middle-income countries, remains underrecognized. This study aimed to assess the prevalence and functional impact of headaches among university students.</p> Methods <p>A cross-sectional study was conducted between Dec 2023 and Dec 2024 among undergraduate students at Delta University of Science and Technology in Egypt. Data was collected using a self-administered questionnaire, which included the demographic data and the Headache Impact Test (HIT-6) to evaluate the effect of headache on daily functions. Descriptive statistics were used to estimate the prevalence and to assess the severity of impact and to further study factors associated with headache impact a generalized mixed effect logistic regression model was used. A P-value of &lt; 0.05 was considered statistically significant.</p> Results <p>A total of 512 university students suffering from headache were included in the analysis. The prevalence of students reported experiencing headaches on the day of the questionnaire was 304 (59.4%). The mean of HIT score was 62.4 ± 6.4, with the majority of students 372 (72.6%) experiencing a severe impact from their headache. Notably, females reported experiencing higher rates of severe headache impact as compared to males (<i>p</i> = 0.008). Despite this, only 140 (27.3%) students had previously sought medical attention for their headaches. Upon using a mixed-effects logistic regression model, stress and light sensitivity was attributed to higher HIT results.</p> Conclusions <p>Headache disorders are highly prevalent among university students with the majority experiencing severe impact from their headache. Despite the high prevalence and impact very few students sought medical consultation. These findings underscore the need for targeted screening, awareness campaigns, and accessible headache management strategies for university students.</p>