We examined the cross-lagged relations between word reading fluency in the two orthographic systems of Japanese: phonetic (syllabic) Hiragana and morphographic Kanji. One hundred forty-two Japanese-speaking children were assessed on word reading fluency twice in Grade 1 (Times 1 and 2) and twice in Grade 2 (Times 3 and 4). Nonverbal IQ, vocabulary, phonological awareness, morphological awareness, and rapid automatized naming were also assessed in Time 1. Results of path analysis revealed that Time 1 Hiragana fluency predicted Time 2 Kanji fluency after controlling for the cognitive skills. Time 2 Hiragana fluency did not predict Time 3 Kanji fluency or vice versa after the autoregressor was controlled, but Hiragana and Kanji fluency were reciprocally related between Times 3 and 4. These findings provide evidence for a cross-script transfer of word reading fluency across the two contrastive orthographic systems, and the first evidence of fluency in a morphographic script predicting fluency development in a phonetic script within the same language.