Human papillomavirus (HPV) causes cervical cancer and sexually transmitted infections. Cervical cancer is the third most common malignancy among the women worldwide. The primary tool for prevention of cervical cancer is through the HPV vaccination. Pre-clinical year medical students must have background knowledge about HPV vaccination as they become healthcare providers, who will play an important role in influencing patients’ decision to receive vaccination. If their knowledge on the HPV is low this will result in poor attitude towards its prevention. This study was aimed to determine the knowledge of HPV vaccine and cervical cancer as well as the acceptance of HPV vaccination among pre-clinical year medical students. A descriptive cross sectional study was conducted among 83 pre-clinical year medical students in National Defence University of Malaysia (NDUM). A set of self-administered questionnaire was distributed to the respondents to gather the data. Although almost half of respondents (46.3%) did not know the exact indication for HPV vaccination Most of them perceived that HPV vaccine can protect against the cervical cancer (64.4%) and it is as important as Hepatitis B or Haemophilus influenzae vaccines in Malaysia (54.9%). Substantial proportion of the respondents (47.6%) disagreed that HPV vaccination will diminish the need for annual Pap smear testing. The findings of this study show that being a pre-clinical year student does not warrant good knowledge and prevention of HPV infection. There is a need to obtain more information about HPV vaccination effects on cervical cancer in their medical school teaching and from the social media.