In 2022, one year after the extension of HPV vaccination to adolescent boys in France, we conducted a qualitative study to explore how French general practitioners (GPs) approach gender-neutral vaccination. Fifteen semi-structured interviews were carried out with private GPs, and a thematic analysis was performed. Thematic saturation was reached at the twelfth interview. Overall, GPs expressed strong support for gender-neutral vaccination, perceiving it as a way to reduce gender-based discrimination and stigmatization. However, important differences emerged in their practices. Recommendations to girls consistently emphasized individual protection against cervical cancer (n = 15), while recommendations to boys (10 out of 15) more often focused on protecting future female partners or referenced risks for men who have sex with men (MSM), rather than emphasizing male-specific cancer risks. Among these GPs, six reported difficulties recommending HPV vaccination to boys, directly linked to the types of arguments they felt were required. Half conveyed inaccurate information, often associating HPV infection exclusively with MSM. These findings highlight gaps in the French approach relative to international guidelines and suggest the influence of gender bias in recommendation practices. Strengthening gender-awareness training and public health messaging may help support more equitable and effective HPV vaccination strategies.