Human papillomavirus (HPV) infection is one of the most common viral infections in sexually active population worldwide, and is the main cause of cervical cancer, which is the fourth most common cancer among women. Serbia ranks third in incidence and mortality rate of cervical cancer in Europe. We conducted a cross-sectional study considering parents’ motivation for the HPV vaccination of their children. Statistical analysis included descriptive statistics and a logistic regression model. We found that the strongest motive was “Recommendation from paediatrician” (20.2%), followed by the attitude that HPV vaccine protects against cancers in different localization (15.4%), the motive “It is better to vaccinate a child than expose them to potential risk of HPV infection” (13.3%) and “Feeling anxiety due to a possible infection and cancer in the child” (13.1%). For those parents that vaccinated their child for some other strongest motive, reasons like “Vaccine is free of charge”, “Recommendation from friends and family” and motive „My child received all obligatory vaccines, so I want to receive this one as well“, were significantly more frequently selected. In the group where paediatricians’ recommendation was not a motive for accepting the HPV vaccine, the largest percentage of parents (89.6%) selected motive “HPV vaccine protects against cancers in different localization” and the motive “It is better to vaccinate a child than expose them to potential risk of HPV infection” (78.1%). Paediatrician’s recommendation is very important for parents’ decision to vaccinate, however, other motives also influenced and had significance in making the parents’ decision to vaccinate their children against HPV. Encouraging trust in public health authorities in Serbia, highlighting the advantages of the HPV vaccine and further encouraging healthcare workers to give stronger recommendations can increase the HPV vaccine uptake. Finally, we provided the basis to create more targeted messages that will empower parents to vaccinate their children.