What is the relationship between literacy skills and implicit learning? To address previous mixed findings, we compared school-aged readers, typical (CON, n = 54) and with dyslexia (DYS, n = 53), in relation to their performance on a serial reaction time task. For the first time, we also included an isolated spelling deficit group (ISD, n = 30) to control for distinctive effects of reading and spelling deficits. A linear reaction times analysis did not reveal between-group differences in implicit learning. However, further examination revealed that most CON (65%) and ISD (63%) were implicit learners, whereas most DYS were nonlearners (64%). Brain activity showed differences in early learning phases: CON learners and DYS nonlearners activated the left inferior frontal gyrus (IFG) and left insula more than other groups. Our findings imply that implicit learning is more frequently disrupted in children with dyslexia than in typical readers, and that activation of the left IFG and insula contributes to effective learning in the latter group but it does not in the former.