Abstract Background The Human papillomavirus (HPV) is a known cause of cervical cancer, and is associated with the development of vaginal, vulvar, anal, penile, and head and neck cancer. The availability of the HPV vaccine has enabled generations of young people to be protected from HPV-related cancers. In 2016, a national immunization program targeting 14-year-old girls and boys has been initiated in Croatia. To date, systematic data on HPV vaccination coverage (VC) in Croatia is lacking. This study aims to determine HPV VC, examine trends in HPV vaccination in Croatia from 2016 to 2023 in the context of the national vaccination program, and assess differences between sexes. Methods The study is designed as a retrospective analysis covering the data from 2016 to 2023, collected from primary healthcare providers. HPV VC within 2000-2008 birth cohorts (BC) are analyzed for all vaccinated with at least one dose and assessed by sex. The trend in HPV vaccination is shown using joinpoint regression. The chi-square for trend is used to compare the vaccination coverage of females (FVC) and males (MVC). The rate ratio between FVC and MVC is calculated. Results HPV VR increased significantly among observed BCs from 6,44 % in 2000 BC to 44,22 % in 2008 BC (FVC rose from 10,67 % to 52,78 %, and males MVC from 2,47 % to 36,05 %). Joinpoint analysis revealed a statistically significant increase in all birth cohorts, while the steeper increase is seen in 2000-2006 BCs (APC = 35,47, P < 0,05) than in 2006-2008 BCs (APC = 13,93, P < 0,05). FVC is significantly higher than MVC in all birth cohorts (Extended Mantel-Haenszel chi-square for linear trend = 809.23, P < 0,001). The highest FVC/MVC rate ratio was observed in the initial 2000 BC (4,31), and the lowest in the last 2008 BC (1,46). Conclusions In Croatia, HPV VC continuously increases among observed BCs. The positive trend is present in both sexes, and the rate ratio between female and male cohorts is decreasing. Key messages • The study presents a systematical overview of HPV vaccination coverage in Croatia from the beginning of the national immunization program, which is crucial for monitoring progress. • In the following years, if the revealed trends persist or advance, Croatia could be closer to reaching Europe’s Beating Cancer Plan concerning eliminating HPV-related diseases.