Background Cervical cancer is one of the most diagnosed and deadly cancers in women globally. Though vaccination is an effective way to reduce cervical cancer, people’s knowledge and acceptance of the vaccination remains a challenge in low and middle-income countries. Therefore, the aim of this study was to assess the level of knowledge and acceptance of Human Papilloma Virus (HPV) vaccination and its associated factors among parents of daughters in Addis Ababa, Ethiopia. Methods A community-based cross-sectional study was conducted among parents or guardians whose daughters are in the age group of 9–17 years and residing in Akaki-Kalty sub-city in Addis Ababa. A multistage sampling technique was used to select the study participants (n = 430). Face-to-face interview was conducted by using a structured questionnaire. Factors associated with the acceptance of HPV vaccination was identified by multivariable binary logistic regression and expressed by adjusted odds ratio (aOR), and respective 95% confidence interval. Results Complete response was obtained from 422 (98.1%) of the participants and their mean age was 39.0 years (SD ± 9.9). Out of the study participants, 41.7% and 72.0% had poor knowledge on cervical cancer and HPV, respectively. More than a quarter (27.0%) of the participants has never heard about HPV vaccine. One-third (36.5%) of the participants had negative attitude towards the HPV vaccine. Overall, 94.3% of the study participants were willing to vaccinate their daughters for HPV. Vaccine acceptability was associated with higher monthly income (aOR = 2.48, 95% CI 1.08–6.34), good knowledge on HPV (aOR = 2.32, 95% CI 1.56–4.87) and the vaccine (aOR = 2.24, 95% CI 1.12–8.60), and positive attitude towards the vaccine (aOR = 5.03, 95% CI 1.63—9.56). Conclusions The overall HPV vaccine acceptance was high. However, two out of five and one-thirds of the parents had poor knowledge on cervical cancer and negative attitude towards the HPV vaccine, respectively. Higher monthly income, good knowledge on HPV and the vaccine, and positive attitude towards the vaccine were associated with acceptance of HPV vaccination. To ensure sustainable acceptance of HPV vaccination, it is crucial to increase the community awareness in a sustainable manner.