Since its adoption into public health programmes in 2006, the Human Papillomavirus (HPV) vaccine has proven its powerful effect in preventing cervical cancer, the most prevalent HPV-associated cancer. Nevertheless, a considerable burden of HPV infection is associated with non-cervical cancers and conditions that, due to a historically gendered narrative around HPV vaccination, are still partially neglected in most preventive agendas. Gender-neutral vaccination (GNV) programmes have been steadily adopted in an increasing number of countries, but global endorsement of this strategy is still being delayed, especially in low- and middle-income countries (LMICs). In this perspective paper, we advocate for an accelerated global shift from female-only to universal, gender-neutral HPV vaccination. This perspective analyses how a GNV strategy addresses the rising burden of non-cervical cancers, promotes gender justice for vulnerabilised groups, and strengthens population-wide herd immunity amidst shifting global funding and healthcare disparities, particularly in LMICs. Further, a gender-neutral approach could also strengthen programme resilience in settings where female vaccination coverage remains far below the elimination targets. The case of HPV vaccination shows that women-only public health interventions can further exacerbate the stigmatisation of women in society and, rather than improving women’s health, amplify inequity. We believe that the experience with the HPV vaccine can play a significant role in demonstrating that women-specific vaccination programmes can have unintended consequences: whilst they may improve specific health outcomes, they simultaneously cause social harm to the sex groups they intend to protect, thereby failing to address broader health outcomes across the global society as a whole.