There is insufficient data on sexually transmitted infections (STI) and related behaviours among key populations, including female sex workers (FSW), in the Pacific region. Using respondent driven sampling, we conducted an integrated bio-behavioural survey with FSW in Vanuatu (aged =18 years) to investigate risk behaviours associations with Chlamydia trachomatis (CT). Weighted population estimates and correlates of CT infection were calculated. Among 149 FSW, prevalence of CT was 36 % (95 % CI 26–48 %). Few FSW reported consistent condom use with recent transactional sex partners (TSP) (8 %; 95 % CI 2–13 %). CT infection was positively associated with increasing number of TSP (adjusted odds ratio [AOR] 1.1; 95 % CI 1.0–1.2) and group sex (AOR 2.9; 95 % CI 1.1–8.2). CT was negatively associated with increasing age of first sex (AOR 0.6; 95 % CI 0.5–0.9) and previous STI treatment (AOR 0.1; 95 % CI 0.0–0.4). A comprehensive public health strategy for prevention and treatment of STI among FSW, incorporating community empowerment strategies, FSW-targeted health services and periodic presumptive treatment, is urgently needed in Vanuatu.