Autism spectrum disorder is associated with high rates of co-occurring health conditions. While elevated prescription rates of psychotropic medications have been reported in the United Kingdom and the United States, there is a paucity of research investigating clinical and prescribing practices in Australia. This study describes the problems managed and medications prescribed by general practitioners in Australia during encounters where an autism spectrum disorder was recorded. Information was collected from 2000 to 2014 as part of the Bettering the Evaluation and Care of Health programme. Encounters where patients were aged less than 25 years and autism spectrum disorder was recorded as one of the reasons for encounter and/or problems managed (n = 579) were compared to all other Bettering the Evaluation and Care of Health programme encounters with patients aged less than 25 years (n = 281,473). At 'autism spectrum disorder' encounters, there was a significantly higher management rate of psychological problems, and significantly lower management rates of skin, respiratory and general/unspecified problems, than at 'non-autism spectrum disorder' encounters. The rate of psychological medication prescription was significantly higher at 'autism spectrum disorder' encounters than at 'non-autism spectrum disorder' encounters. The most common medications prescribed at 'autism spectrum disorder' encounters were antipsychotics and antidepressants. Primary healthcare providers need adequate support and training to identify and manage physical and mental health concerns among individuals with autism spectrum disorder.