Introduction: Baseline information on knowledge, attitude and practice towards HPV vaccination is crucial to establish a progress track on the current HPV immunization program. Aims: This study was designed to assess the knowledge, attitude and practice towards human papillomavirus (HPV) infection, cervical cancer and HPV vaccination practice among secondary school students in rural areas of Negeri Sembilan, Malaysia. Methods: A cross sectional study was conducted in several schools in rural areas of Negeri Sembilan, Malaysia. The respondents were selected using simple random sampling method. Data was collected by face-to-face interview using standardized and validated questionnaire. Data analysis was done using SPSS version 21.0. Results: A total of 380 respondents participated in this study. Females scored significantly higher for the knowledge items compared to the males. Majority of respondents (86.6%) indicated their intention to get HPV vaccines. Willingness to be vaccinated was significantly associated with the level of knowledge of cervical cancer (AOR 1.658; 95% CI 1.018-2.698; p=0.042). Gender (AOR 3.289; 95% CI 1.999-5.412; p<0.001) is a significant predictor for someone who rejects vaccination due to side effects. In this study, 89.8% of female respondents had been vaccinated against HPV. Conclusion: Respondents showed poor knowledge level despite high HPV vaccination practice. Intention to get vaccinated was significantly associated with knowledge of cervical cancer. Therefore, it is necessary to educate the community members on HPV and HPV vaccine as HPV vaccination is the most effective way to prevent cervical cancer and its related diseases.