This is a cross-sectional study of 399 subjects conducted to explore the association between drug use and risk behaviour for HIV and sexually transmitted infections (STIs) among female sex workers (FSWs), and also to study the prevalence of HIV/STIs among drug-using FSWs (DUFSWs) and non-DUFSWs in Yunnan province of China. Demographic information, mobility, sexual and drug-using behaviours were collected and subjects were tested for HIV/STIs. Mean age was 27 years (SD = ±7.8) and 94 (23.6%) tested positive for recent opiate use. Compared with non-DUFSWs, DUFSWs had a significantly higher prevalence of HIV (38% versus 4%, P ≤ 0.001), herpes simplex virus type 2 (HSV-2; 92% versus 60%, P ≤ 0.001) and STIs (95.7% versus 69.2%, P ≤ 0.001). DUFSWs had a significantly longer duration of commercial sex work compared with non-DUFSWs (median 5 versus 1 years, P ≤ 0.001), and had at least two clients in the last working day. DUFSWs were also more likely to work in low-end commercial sex venues and frequented a greater number of work locations than non-DUFSWs. Compared with non-DUFSWs, DUFSWs were more likely to exhibit riskier sexual behaviours and greater workplace mobility. Interventions targeting drug-related behavioural changes are needed urgently in this population in order to reduce rates of HIV and STIs.