Background Female sex workers in Australia have achieved some of the lowest documented prevalences of human immunodeficiency virus (HIV) and other sexually transmissible infections globally but rates overall are increasing in Australia and warrant closer investigation. Methods We constructed a retrospective cohort using repeat testing data extracted from a network of 42 sexual health clinics. Poisson and Cox regression were used to determined trends in incidence and risk factors for HIV, chlamydia, gonorrhoea, and infectious syphilis among female sex workers. Results From 2009 to 2015, 18,475 women reporting sex work attended a participating service. The overall incidence of urogenital chlamydia was 7.7/100 person years (PY), declining by 38% from 2009 to 2013 before increasing by 43% to 2015 (P < 0.001); anorectal chlamydia incidence was 0.6/100 PY, and pharyngeal was 1.9/100 PY, which increased significantly during the study period (P < 0.001, both). For gonorrhoea, the urogenital incidence was 1.4/100 PY, anorectal incidence was 0.3/100 PY, P < 0.001), and 3.6/100 PY for pharyngeal; urogenital incidence doubled during the study period, anorectal increased fivefold, and pharyngeal more than tripled (P < 0.001, all). Incidence of infectious syphilis was 0.4/100 PY, which remained stable from 2009 to 2015 (P = 0.09). There were seven incident infections of HIV among female sex workers (0.1/100 PY). Inconsistent condom use with private partners, higher number of private partner numbers, recent injecting drug use, younger age, and country of birth variously predicted sexually transmissible infections among female sex workers. Conclusions Although infectious syphilis and HIV remain uncommon in female sex workers attending Australian sexual health clinics, the increasing incidence of gonorrhoea across anatomical sites and increasing chlamydia after a period of decline demands enhanced health promotion initiatives.