She used to be late for school often.

Literal

[topic-は] often school [to-に] was-late.

遅刻する ('to be late') takes に for the destination/event one is late for — に marks the target of the lateness. Notable cultural context: punctuality is taken seriously in Japanese school culture, with morning gates often closing precisely on time and tardiness recorded as a formal blemish. 遅刻 stands as a culturally weighty noun in school discipline contexts.