Early sensory deprivation allows assessing the extent of reorganisation of cognitive functions, well beyond sensory processing. As such, it is a good model to explore the links between sensory experience and cognitive functions. One of these functions, statistical learning – the ability to extract and use regularities present in the environment – is suspected to be impaired in prelingually deaf children with a cochlear implant. However, empirical evidence supporting this claim is very scarce and studies have reported contradictory results. This might be because previous studies have tested statistical learning only in the visual modality and did not make clear distinctions between multiple types of statistical regularities. To overcome these problems, we designed a modified serial reaction time task where cochlear implanted children and normal hearing children had to react to auditory sequences that embed multiple statistical regularities, namely transition probabilities of 0th, 1st or 2nd order. We compared the reaction times of the children with the output of a simple computational model that learns transition probabilities. First, 6–12 years old children were able to learn 0th and 1st order transition probabilities but not 2nd order ones. Second, there were no differences between cochlear implanted children and their normal hearing peers. These results indicate that auditory statistical learning is preserved in congenitally deaf children with cochlear implants. This suggests in turn that early auditory deprivation might not be crucially detrimental for the normal development of statistical learning.