We found uptake of inactivated influenza vaccine (IIV) in pregnancy in remote-living Aboriginal and Torres Strait Islander women from the NT of Australia was 0% for the pre-influenza A (H1N1) pandemic period (A (H1N1) pdm09) from 2003 to 2006, and remained unacceptably low (7%) for the post-influenza A (H1N1) pdm09 period (> 2009–2011). Although IIV was routinely recommended for pregnant women throughout the entire eight year study period, vaccine uptake was extremely low among the 697 pregnancies in our study, particularly in women with known comorbidities and/or high risk factors.