The precise relation between implicit learning and reading abilities has not been determined yet, given the limited research on implicit learning between typically developing (TD) students and those with reading difficulties (RD). Additionally, the influence of modality-related implicit learning performance in children remains largely unknown. To investigate implicit learning performance across different sensory modalities in TD and RC students. Implicit learning was assessed using an Artificial Grammar Learning paradigm (AGL). In total 26 children (F = 10) of which, 15 TD (M = 8.3, SD = 1.1 years) and 11 RC children (M = 7.7, SD = 1.1 years) were tested in three different AGL modalities (visual, auditory, and tactile), and underwent evaluation using a battery of cognitive measures related to reading skills. Statistically significant cross-group differences were found for visual and for auditory stimuli. In line with this, reading correlated positively with learning in the auditory modality and phonological awareness with visual modality. The results indicate that reading challenges might relate to impairments in implicit learning across more than one domain, particularly impacting the acquisition of auditory and visual non-verbal material. Building upon these findings the potential educational applications are discussed.