To describe the key elements of a comprehensive sexual health program implemented between 2002 and 2005 in remote Indigenous communities on the Tiwi Islands and to assess its effectiveness in reducing rates of bacterial sexually transmitted infections (STIs). A descriptive study using STI notification and laboratory testing data to analyse the occurrence of STI diagnoses overtime compared to nearby similar regions. Over the four years' of program implementation, the numbers of tests and individuals tested increased substantially and were sustained. The notification rate of chlamydia decreased from 1,581.3 to 80.0 per 100,000, that of gonorrhoea from 2,919.2 to 1,159.7 and that of syphilis from 1,743.4 to 200.0, representing a decrease of 94.9%, 60.2% and 88.5%, respectively. No similar trends in notification rates were observed in nearby regions. During the same time, the positivity rate (the number of positive tests divided by the total number of tests) of nucleic acid tests for gonorrhoea decreased from 5.9% (56/952) to 3.9% (39/1,004), and that for chlamydia decreased from 5.2% (38/1,003) to 0.3% (3/1,007), representing a decrease of 33.9% and 94.2%, respectively. The Tiwi Sexual Health Program was accompanied by a significant reduction in STI rates between 2002 and 2005. This model of a comprehensive sexual health program with a dedicated co-ordinator located within a Primary Health Care service can be recommended as an effective approach to address high rates of STIs in remote Indigenous community settings.