Background Availability of effective vaccine against cervical cancer is not synonymous with effective control program. Awareness and knowledge of the vaccine is pertinent to its uptake. It is important to identify possible barriers to successful HPV vaccination program among young people. Materials and Methods A cross-sectional study of 572 female students selected by probability sampling technique from two Universities in South West, Nigeria was carried with the use of self-administered questionnaire. Results The proportion of respondents who were able to correctly identify risk factors for cervical cancer ranged from 14.3% (increasing age) to 53.5% (Chlamydia infection). Less than 50% of the participants were found to be knowledgeable about all the knowledge themes except the preventable nature of cervical cancer of which 62.9% were knowledgeable. The commonest sources of information were health care providers and seminars (44.1% each). Three hundred and forty-six (60.5%) respondents were willing to receive the vaccine. Age, faculty, age at menarche, awareness of HPV infection and cervical cancer; and all the knowledge themes except the need for male vaccination shows statistically significant relationship with acceptability of HPV vaccine (p < 0.05). Possible barrier to successful implementation of HPV vaccination program among young people in Nigeria were also identified. Inadequate information was thought to be the major barrier (68.9%). The other barriers were cost (38.1%), worry about possible complications (15.0%) and vaccine efficacy (13.3%); and lack of parental consent for vaccination (12.9%). Conclusion Knowledge of HPV vaccine is poor but its acceptability is high. Successful HPV vaccination program will depend on innovative and multi-pronged campaign that addresses various misconceptions about the vaccine. Economic accessibility of the vaccines also needs to be enhanced.