Gender disparities in testing rates for sexually transmitted infections (STIs) have been identified as one potential factor sustaining high rates of STIs and repeat infections in the Northern Territory of Australia, especially in remote Indigenous communities. The study aimed to investigate the reasons for these disparities utilising a mixed-method study design. We conducted an audit on client information at a remote community health clinic, focus-group discussions with young men in the same community and interviews with experienced remote area clinicians. The clinic audit found a significantly higher proportion of female residents of the community than males visited the clinic (72.8 versus 55.3%, p < 0.005). Women were also more likely to be tested for STIs than men when visiting the clinic (49.7 versus 40.3%, p = 0.015). Major barriers to men’s seeking STI testing included a sense of shame from being seen visiting the clinic by women, men’s lack of understanding of STIs and the need for testing, and inadequate access to male clinicians. Increasing men’s access to healthcare and STI testing requires offering testing at a gender-sensitive and separate locations, and community-based sexual health promotion to increase knowledge of STIs.