Objective To identify primary care recorded factors associated with the short-term human papillomavirus (HPV) vaccination among girls and female adolescents. Methods We used the Spanish Pharmacoepidemiological Research Database for Public Health System to identify girls aged 9-18 years in 2007-2016 with ≥1 year of primary care data (start date) and collect baseline characteristics and consultations. The link between those factors and the 1-year HPV vaccination was assessed through multivariate adjusted Odds Ratios (OR; 95% CI). Results Among 388,669 girls identified, 14,999 were vaccinated against HPV during the first year. The vaccination decreased among girls consulting for social (0.62; 0.55-0.70) or adaptation (0.60; 0.38-0.93) problems, prescriptions of benzodiazepines (0.58; 0.35-0.94) or drugs for gastrointestinal symptoms (0.58; 0.38-0.89), with recorded tuberculosis test (0.68; 0.52-0.87), B and C meningitis (0.46; 0.43-0.50) vaccination, consulting the doctor in the last 3 months (0.92; 0.87-0.98) and with severe thinness (0.68; 0.59-0.78) or obesity (0.88; 0.78-0.99). The odds increased among girls with abdominal pain (1.10; 1.04-1.16), prescriptions in the last 3 months (1.17; 1.10-1.25), and vaccinations against chickenpox (1.16; 1.07-1.27), influenza (1.23; 1.08-1.40), hepatitis (1.46; 1.35-1.58) and diphtheria-tetanus (1.91; 1.82-2.01). Conclusions The correlation between the HPV and other vaccinations suggested medical (contra)indications or willingness and knowledge/beliefs that might affect different vaccinations similarly. The higher frequency of the HPV vaccination among females requiring specific treatments or with abdominal pain suggested vulnerability to HPV complications. While a decreased HPV vaccination linked to certain social and personal situations (and benzodiazepines treatment) requires further research.