Background and Objectives: Vaccine hesitancy has been rated among the top 10 global Public Health threats by the World Health Organization (WHO). Causes of vaccine hesitancy are heterogeneous and the media environment can negatively influence vaccination acceptance and contribute to vaccine hesitancy. The purpose of this study was to determine the association between eHealth literacy and vaccine hesitancy towards flu and HPV among non-health colleges students at King Faisal University. Methods: This analytical cross-sectional study obtained data from 876 non-health undergraduates at King Faisal University selected through two-stage cluster sampling procedure. Two validated instruments, particularly, the eHealth Literacy Scale (eHEALS) and the Adult Vaccine hesitancy Scale were used. Statistical analysis was done using JASP. Logistic regression was performed to determine the association between the student’s level of eHealth literacy and vaccine hesitancy towards flu and HPV. Results: Half of the students had high eHealth literacy level. The estimated proportion of students who displayed hesitancy towards the HPV and flu vaccine was 52.85% (95%CI=49.49%-56.20%) with the statement “I am concerned about serious adverse effects of vaccines” (89% CI: 87.00%-91.00%) as the most prevalent reason for vaccine hesitancy. Students with high eHealth literacy were roughly three times more likely to be not vaccine hesitant (p < .001) compared to those with low eHealth literacy. Conclusions: The present data confirms that eHealth literacy was significantly associated with vaccine hesitancy which necessitates the university to take initiatives to further enhance the eHealth literacy levels of the non-health students by utilizing the electronic platforms to share credible health information. The Ministry of Health should also enhance their social media presence in order to spread reliable health information, specifically regrading vaccines and their safety.