In Nigeria, women are underrepresented in senior leadership roles despite dominating the health workforce. Men occupy most decision-making positions in a system that has kept women on the sidelines of leadership for decades. This gender disparity in leadership is not limited to the health sector. Women are also underrepresented in political leadership and other areas. The barriers to women’s leadership in Nigeria’s public health organizations abound and arise from individual, societal, cultural, religious, and organizational factors. Gender disparity in health sector leadership impacts health outcomes. Therefore, stakeholders must identify critical barriers to gender parity in leadership and explore opportunities to increase the proportion of women in senior leadership roles in the health sector.