Self-injurious behaviour is purportedly common in autism, but prevalence rates have not yet been synthesised meta-analytically. In the present study, data from 14,379 participants in thirty-seven papers were analysed to generate a pooled prevalence estimate of self-injury in autism of 42% (confidence intervals 0.38–0.47). Hand-hitting topography was the most common form of self-injury (23%), self-cutting topography the least common (3%). Sub-group analyses revealed no association between study quality, participant intellectual disability or age and overall prevalence rate of self-injury. However, females obtained higher prevalence rates than males ( p = .013) and hair pulling and self-scratching were associated with intellectual disability ( p = .008 and p = .002, respectively). The results confirm very high rates of self-injury in autism and highlight within group risk-markers. Electronic supplementary material The online version of this article (10.1007/s10803-020-04443-1) contains supplementary material, which is available to authorized users.