Background With competing interests, limited funding and a socially conservative context, there are many barriers to implementing evidence-informed HIV prevention programmes for sex workers and injection drug users in Pakistan. Meanwhile, the HIV prevalence is increasing among these populations across Pakistan. We sought to propose and describe an approach to resource allocation which would maximise the impact and allocative efficiency of HIV prevention programmes.

Methods Programme performance reports were used to assess current resource allocation. Population size estimates derived from mapping conducted in 2011 among injection drug users and hijra, male and female sex workers and programme costs per person documented from programmes in the province of Sindh and also in India were used to estimate the cost to deliver services to 80% of these key population members across Pakistan. Cities were prioritised according to key population size.

Results To achieve 80% population coverage, HIV prevention programmes should be implemented in 10 major cities across Pakistan for a total annual operating cost of approximately US$3.5 million, which is much less than current annual expenditures. The total cost varies according to the local needs and the purchasing power of the local currency.

Conclusions By prioritising key populations at greatest risk of HIV in cities with the largest populations and limited resources, may be most effectively harnessed to quell the spread of HIV in Pakistan.