ABSTRACT This study investigated the role of prosody and word order in identifying the focus of sentences in Japanese. Native Japanese speakers listened to sentences with different types of word order (subject–object–verb (SOV) vs. object–subject–verb (OSV)), prosody (whether the first noun phrase is stressed or not) and preceding contexts (object- vs. subject-wh questions), while processing costs were measured using pupillometry. Although syntactically non-basic OSV was more difficult to process than basic SOV, this processing difficulty was considerably reduced when the supportive context (the subject-wh question) required S to be focused. The time–course analysis of pupillometry revealed that the Japanese speakers immediately used prosodic cues to determine the focus of sentences, but the effect of word order cues for focus was delayed until the sentence-final verb was encountered. This study advances our understanding of the temporal dynamics of focus processing and the interplay between syntactic and information structures in sentence comprehension.