Fluent reading requires successfully mapping between visual orthographic and auditory phonological representations and is thus an intrinsically cross-modal process, though reading difficulty has often been characterized as a phonological deficit. However, recent evidence suggests that orthographic information influences phonological processing in typical developing (TD) readers, but that this effect may be blunted in those with reading difficulty (RD), suggesting that the core deficit underlying reading difficulties may be a failure to integrate orthographic and phonological information. Twenty-six (13 TD and 13 RD) children between 8 and 13 years of age participated in a functional magnetic resonance imaging (fMRI) experiment designed to assess the role of phonemic awareness in cross-modal processing. Participants completed a rhyme judgment task for word pairs presented unimodally (auditory only) and cross-modally (auditory followed by visual). For typically developing children, correlations between elision and neural activation were found for the cross-modal but not unimodal task, whereas in children with RD, no correlation was found. The results suggest that elision taps both phonemic awareness and cross-modal integration in typically developing readers, and that these processes are decoupled in children with reading difficulty.