Pre-registration refers to the practice of researchers preparing a time-stamped document describing the plans for a study. This open research tool is used to improve transparency, so that readers can evaluate the extent to which the researcher adhered to their original plans and tested their theory appropriately. In the current study, we conducted an audit of pre-registration in autism research through a review of manuscripts published across six autism research journals between 2011 and 2022. We found that 192 publications were pre-registered, approximately 2.23% of publications in autism journals during this time frame. We also conducted a quality assessment of a sample of the pre-registrations, finding that specificity in the pre-registrations was low, particularly in the design and analysis components of the pre-registration. In addition, only 28% of sampled manuscripts adhered to their analysis plan or transparently disclosed all deviations. Autism researchers conducting confirmatory, quantitative research should consider pre-registering their work, reporting any changes in plans transparently in the published manuscript. We outline recommendations for researchers and journals to improve the transparency and robustness of the field.