The highly remote pastoralist communities in Kaokoland, Namibia, have long been presumed to have high gonorrhoea prevalence. To estimate gonorrhoea prevalence and correlates of infection, we conducted a cross-sectional study of 446 adults across 28 rural villages. Gonorrhoea status was determined from urethral and vaginal swabs via qPCR assay. All participants answered a closed-ended interview about demographics, sexual behaviour and symptom history. Sixteen per cent of participants had high-level infections (⩾ID(50) dose) and 48% had low-level infections (<ID(50) dose). Women had higher prevalence than men of both high- and low-level infections. High-level infections were regionally and seasonally clustered, occurring in young adults in the Ehama region during the winter. Low-level infections were distributed homogenously across demographic characteristics, season, and region. All low-level infections and most high-level infections (men 78%, women 95%) were asymptomatic and left untreated. The epidemic-like nature of high-level gonorrhoea cases suggests that intervention efforts can be focused on seasons of high social activity.