We examined whether developing reading skills in the two scripts of Japanese, syllabic Hiragana and morphographic Kanji, had differential effects on underlying cognitive skills. One hundred ninety-one Japanese children (97 girls, 94 boys; M[subscript age] = 100.23 months) were assessed on rapid automatized naming (RAN), vocabulary, morphological awareness, visual-spatial skills, Hiragana reading fluency, and Kanji character recognition at the end of Grade 2 and again at the end of Grade 3. Results of cross-lagged analysis showed that Hiragana reading fluency in Grade 2 predicted RAN and visual-spatial skills in Grade 3, and Kanji character recognition in Grade 2 predicted vocabulary in Grade 3, even when the same skills in Grade 2 were controlled. Taken together, these findings suggest that the nature of the script children learn can influence how developing reading skills affect their cognitive underpinnings.