For almost two decades, diagnosis rates of sexually transmitted infection (STI) such as chlamydia and gonorrhoea have been notably higher for residents of remote Indigenous communities than for non-Indigenous Australians. High levels of population movement between remote communities may be a contributing factor in sustaining these high rates. We developed an individual-based computer simulation model to study the relationship between population movement and the persistence of STIs within multiple small communities. We examine the distribution of infection across locations and the impact of mobility and periodicity on prevalence over a range of location- and time-specific screening interventions. Our findings suggest that: 1) short-term population movement, along with periodic variations in travel patterns allow STIs to persist at a high level in multiple small populations; 2) infection is not evenly distributed across populations, with more than 80% of infection concentrated at the most populous location, despite this locations only comprising 72% of the total population at a given time; 3) maintaining screening coverage at the current level (44% of population screened annually) in small locations alone has limited impact on STI prevalence in the overall population; reduction in prevalence is unlikely to be achieved unless screening coverage and frequency are increased substantially or screening is expanded to include larger regional centres prevalence is higher; 4) population mobility can influence the outcomes of location- and time-specific screening interventions; interventions should be scheduled to occur during periods of low mobility when individuals are more likely to be at home and have access to local health services.