She whispered something in his ear.

Literal

She [topic-は] him [to-に] something ear-whisper [object-を] did.

耳打ち (みみうち) literally 'ear-hit' = 'whispering into the ear.' Vivid kanji choice — 打 ('hit, strike') captures the close, focused contact of mouth-to-ear delivery. As a noun-plus-する verb, 耳打ちをする / 耳打ちする both work. Often implies secret or private communication.