Personal trainers are a popular source of exercise guidance for the public but have been shown to have fundamental errors in their knowledge, and hold misconceptions about some exercise and nutritional concepts. Critical thinking skills have been found to relate inversely to misconceptions in other populations but this has not been examined in personal trainers. This study assessed the impact of an online, domain-specific, critical thinking course on the misconceptions and critical thinking ability (CTA) of personal trainers. One hundred and twenty-five participants were recruited into a randomised control trial. Participants completed measures of knowledge, misconceptions, CTA, and their use and perceived trustworthiness of sources of information about exercise and nutrition, then were allocated to either an intervention or control group. The intervention group completed the course over six weeks, while the control group waited six weeks before being surveyed again. Participants showed reduced endorsement of misconceptions and increased trust in reliable sources after completing the intervention. CTA improved in both the intervention and control groups. These results provide evidence that targeting critical thinking skills tailored to relevant content may contribute positively to the professional development of personal trainers.