Despite the availability of a safe and effective vaccination, uptake of human papillomavirus (HPV) vaccination remains low worldwide. We aimed to analyze the coverage of HPV immunization during the first year of the immunization program and the sociodemographic characteristics across different administrative units in Serbia and Montenegro. Coverage of HPV vaccination in Serbia for females aged 9-14 and 15-19 years was 5.5% and 5.9%, respectively. The coverage rate of immunization against HPV in Montenegro for girls aged 9-14 years was 22.1%. Within Serbia, only one administrative region (Moravica) had HPV immunization coverage in girls 9-19 years old above 10%, 11 districts had coverage from 5 to 10%, while 13 districts had coverage below 5%. As per Montenegro, two administrative units, Cetinje and Berane, reported the highest coverage, with 39% and 36.4% of vaccinated eligible girls, respectively. When we explored the coverage of HPV immunization among girls aged 9-19 years across different regions in Serbia, we observed that the level of coverage did not correlate with the number of pediatricians or with the population density. In Montenegro, we observed a similar situation. On the other hand, we noticed a statistically significant moderate negative correlation (r = -0.446; p = 0.026) between HPV immunization coverage and the percentage of illiterate women in the administrative units. Comparing the coverage between the two countries we found that the higher coverage in Montenegro corresponded with a smaller number of female populations aged 9-14 years, with higher average net monthly income, with smaller population density and smaller number of pediatricians, among divorced persons, and among those without formal education or incompletely primary education. Taking into account the experiences in Montenegro, increasing immunization coverage in Serbia could be achieved through a more vigorous educational campaign targeting schools, the general population, and healthcare workers as well as by additionally incentivizing those engaged in these activities.