A national tax increase, which became known as the “alcopops tax”, was introduced in Australia on the 27th April 2008 on ready-to-drink alcoholic beverages, which are consumed predominantly by young people. The affordability of alcohol has been identified as the strongest environmental driver of alcohol consumption, and alcohol consumption is a well-known risk factor in the spread of sexually transmitted infections via its association with sexual risk-taking. We conducted a study to investigate whether there was any association between the introduction of the tax and changes in national chlamydia rates: (i) notification rates (diagnoses per 100,000 population; primary outcome and standard approach in alcohol taxation studies), and (ii) test positivity rates (diagnoses per 100 tests; secondary outcome) among 15–24 and 25–34-year-olds, using interrupted time series analysis. Gender- and age-specific chlamydia trends among those 35 and older were applied as internal control series and gender- and age-specific consumer price index-adjusted per capita income trends were controlled for as independent variables. We hypothesised that the expected negative association between the tax and chlamydia notification rates might be masked due to increasing chlamydia test counts over the observation period (2000 to 2016). We hypothesised that the association between the tax and chlamydia test positivity rates would occur as an immediate level decrease, as a result of a decrease in alcohol consumption, which, in turn, would lead to a decrease in risky sexual behaviour and, hence, chlamydia transmission. None of the gender and age-specific population-based rates indicated a significant immediate or lagged association with the tax. However, we found an immediate decrease in test positivity rates for 25–34-year-old males (27% reduction—equivalent to 11,891 cases prevented post-tax) that remained detectable up to a lag of six months and a decrease at a lag of six months for 15–24-year-old males (31% reduction—equivalent to 16,615 cases prevented) following the tax. For no other gender or age combination did the change in test positivity rates reach significance. This study adds to the evidence base supporting the use of alcohol taxation to reduce health-related harms experienced by young people and offers a novel method for calculating sexually transmitted infection rates for policy evaluation.