Background: Headache is one of the common health problems in the world which can be frequently seen among undergraduates. The current research was mainly focused to explore the prevalence of headaches among undergraduates in Sri Lanka.Method: This cross-sectional survey-based study was conducted among undergraduates of five Sri Lankan universities including various disciplines from science to non- science. A purposive sample of undergraduates was recruited to complete a self-administered questionnaire after obtaining their consent. Data were analyzed using Statistical Package for the Social Sciences (SPSS v25 IBM, New York, USA) and the significant differences among variables were assessed by using Chi-square test. Ethical approval was obtained from the Ethical Review committee of Faculty of Allied Health Sciences, University of Peradeniya, Sri Lanka.Results: The majority of respondents were males (51%, n=146) and who were following science courses (55%, n=158). Undergraduates (76%, n=218) had experienced headache. Common trigger factors were stress related to work (72%, n=171), mental fatigue (54%, n=129), and sleeplessness (33%, n=79). Undergraduates 43% (n=123) who perceived the experience of headache sought the treatments. Usage of non-prescribed medication was significantly high (73, n=90) among them. There was a statistically significant difference between the occurrence of headache for non-science students with the participation for lectures (p=0.021); health status with the academic year (p=0.00); perceived current headache problem with gender (p=0.03) and the avoidance in participating lectures with academic years (p=0.006). Conclusions: It can be concluded that most undergraduates in Sri Lankan universities have been affected by headaches. Stress-related to work, Irregular sleep behavior, mental fatigue and prolonged computer work were the most common trigger factors for headaches among undergraduates in Sri Lanka.