Despite national policies to support sexual rights, Timorese women are constrained when making sexual and reproductive health decisions. Contextual understanding of sexual decision making is vital for effective engagement by sexual and reproductive health service providers with communities. An intersectional reproductive justice approach broadens the sexual rights lens allowing for an examination of multi-system factors impacting on sexual rights and health. Using the Matrix of Domination as a conceptual framework, we explored Timorese perceptions around decisions to have sex, and examined intersecting systems of oppression impacting on these decisions. Our study adopted a critical medical anthropological approach using ethnographic methods. A decolonising methodology aimed to make Timorese worldviews central to the analysis. Nine focus group discussions with 80 men and 17 individual reproductive history interviews with women were held in 4 of Timor-Leste’s 13 municipalities during October 2015. Findings suggest that decisions to have sex are framed in terms of wishes and rights; however, it was the perceived entitlements of men that were prioritised and predominantly men who made these decisions. Violence, coercion and unwanted pregnancies were linked to decisions about sex, and identified as potential consequences for women, impacting on women’s health and sexual rights.