Worldwide recognition of gender inequality and discrimination following the #MeToo movement has been slow to reach the field of global health. Although international institutions have begun to address gender, the perspectives of front-line global health workers remain largely undocumented, especially in regions not captured by large-scale surveys. Long-term collaborative relationships between clinicians and educators participating in paired institutional partnerships can foster cross-cultural dialogue about potentially sensitive subjects. King’s Somaliland Partnership (KSP) has linked universities and hospitals in Somaliland and London, UK, for health education and improvement, since 2000.We collaboratively developed an anonymous, mixed methods, online survey to explore workplace experiences among Somaliland and UK-based staff and volunteers. We adapted the Workplace Prejudice/Discrimination Inventory to address gender inequality, alongside qualitative questions. Somaliland (but not UK) women reported significantly more gender prejudice and discrimination than men (medians=43 and 31, z=2.137, p=0.0326). While front-line Somaliland workers described overt gender discrimination more frequently, UK respondents reported subtler disadvantage at systemic levels. This first survey of its kind in Somaliland demonstrates the potential of global health partnerships to meaningfully explore sensitive subjects and identify solutions, involving a range of multidisciplinary stakeholders. We propose priority actions to address pervasive gender inequality and discrimination, including wider engagement of academia with gender-focused research, institutional actions to address barriers, national prioritisation and nurturing of grassroots initiatives, through institutional partnerships and international networks. Without sustained, concerted intervention across all levels, gender inequality will continue to hinder progress towards the vision of good health for all, everywhere.