Context-specific typologies of female sex workers (FSWs) are essential for the design of HIV intervention programming. This study develops a novel FSW typology for the analysis of transactional sex risk in rural and urban settings in Indonesia. Mixed methods include a survey of rural and urban FSWs (n = 310), in-depth interviews (n = 11), key informant interviews (n = 5) and ethnographic assessments. Thematic analysis categorises FSWs into 5 distinct groups based on geographical location of their sex work settings, place of solicitation, and whether sex work is their primary occupation. Multiple regression analysis shows that the likelihood of consistent condom use was higher among urban venue-based FSWs for whom sex work is not the only source of income than for any of the other rural and urban FSW groups. This effect was explained by the significantly lower likelihood of consistent condom use by rural venue-based FSWs (adjusted OR: 0.34 95% CI 0.13–0.90, p = 0.029). The FSW typology and differences in organisational features and social dynamics are more closely related to the risk of unprotected transactional sex, than levels of condom awareness and availability. Interventions need context-specific strategies to reach the different FSWs identified by this study's typology.