Despite the end of civil war in 2005, many people in South Sudan continued to experience deep insecurity and forms of violent conflict. This sense of insecurity was exacerbated by the lack of state protection and perceived injustice in power distribution at the national level. Based on a 2013 study prior to the country’s relapse into large-scale violence, this article discusses gendered insecurity and agency among the Latuko in Imatong state. In response to their sense of insecurity, the Latuko have developed security arrangements representing forms of hybrid security governance. Using a notion of masculinity, the article reflects on the gender dynamics in these local security arrangements and shows that social order created by customary institutions can contribute to an increase in violence against women at the domestic level. And while women are excluded from the decision-making institutions governing security arrangements, they exercise subtle forms of agency to influence them.