Developmental dyslexia (DD) is defined as difficulties in learning to read even with normal intelligence and adequate educational guidance. Deficits in implicit sequence learning (ISL) abilities have been reported in children with DD. We investigated brain plasticity in a group of 17 children with DD, compared with 18 typically developing (TD) children, after two sessions of training on a serial reaction time (SRT) task with a 24-h interval. Our outcome measures for the task were: a sequence-specific implicit learning measure (ISL), entailing implicit recognition and learning of sequential associations; and a general visuomotor skill learning measure (GSL). Gray matter volume (GMV) increased, and white matter volume (WMV) decreased from day 1 to day 2 in cerebellar areas regardless of group. A moderating effect of group was found on the correlation between WMV underlying the left precentral gyrus at day 2 and the change in ISL performance, suggesting the use of different underlying learning mechanisms in DD and TD children during the ISL task. Moreover, DD had larger WMV in the posterior thalamic radiation compared with TD, supporting previous reports of atypical development of this structure in DD. Further studies with larger sample sizes are warranted to validate these results.