Objectives We examined data collected as part of the fifth round of integrated biological and behavioural surveillance to determine the prevalence and factors associated with HIV infection among female sex workers (FSWs) in Pakistan.

Methods FSWs were defined as ‘all females, age 13 years and above, who receive money or goods in exchange for sexual services, regardless of the site of operation’. Data were collected between October 2016 and January 2017 in 18 cities using multistage sampling techniques to randomly select FSWs from spots facilitated by peers. Behavioural data were collected by interviewers using structured questionnaires, which was followed by obtaining finger prick blood samples tested for HIV using two rapid tests. Multivariate logistic regression analysis was done to assess independent associations of potential correlates using HIV status as dependent variable.

Results We invited 5728 FSWs to participate, of which 68 refused to participate (refusal rate=1.2%). Of the 5660 FSWs who participated, 121 were HIV seropositive (weighted HIV prevalence 2.3%; 95% CI 1.9% to 2.7%) mostly concentrated within cities in Sindh. Multivariate analysis showed being uneducated/illiterate (adjusted OR (aOR) 2.1; 95% CI 1.4 to 3.4), directly dealing with clients without a pimp (aOR 1.8; 95% CI 1.1 to 2.8), non-use of condom with clients (aOR 1.8; 95% CI 1.1 to 2.8), having sexual contact with people who inject drugs (PWID) (aOR 2.2; 95% CI 1.3 to 3.7) and non-participation in HIV programmes (aOR 1.7; 95% CI 1.0 to 3.1) as factors independently associated with HIV seropositivity.

Conclusions We found a weighted national HIV prevalence of 2.3% and identified factors independently associated with HIV in FSWs. The country needs to scale up HIV prevention programmes to improve coverage, prioritising FSWs who are illiterate, work independently and have PWID as sex partners. Emphasis should be laid on strategies to improve condom use with both regular and non-regular partners.