Autistic children and adults are at increased risk of showing behaviours that may be described as challenging, however, little is known about whether or how these behaviours may change over time. Given the profound impact that challenging behaviour can have on both the autistic individual and their support network, it is critical that the trajectory of challenging behaviours be better understood. This systematic review and meta-analysis identified and synthesised observational longitudinal studies of challenging behaviour in autistic individuals. Fifty-six studies were included in the systematic review, and the effect sizes of 37 independent samples arising from 34 of these reports were examined through meta-analysis. Crucially, across the 37 samples, scores on the measures of challenging behaviour reduced by a small, yet significant, extent over time. Although age of the sample at baseline assessment did not moderate the effect, the time between the baseline assessment and final follow-up and age at final follow-up both moderated the magnitude of the effect, with challenging behaviour scores reducing to a larger extent in (a) studies with longer intervals between baseline and final follow-up and (b) studies with older samples at follow-up. The results from the current systematic review and meta-analysis have both theoretical and practical implications for understanding challenging behaviour over time in autistic individuals. Avenues for future research are also highlighted that may allow better understanding, and therefore support of, challenging behaviour in autistic individuals.