Emergency services responded to reports a ute had rolled on Moulamein Road at Moulamein, about 110 kilometres from Deniliquin, just after 12pm.
NSW Police said when arrived they found a Toyota Hilux with significant damage.
The six-year-old boy died at the scene while the four-year-old was treated by paramedics from both NSW and Victoria.
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The surviving child was flown to Melbourne Children’s Hospital.
“The driver, a 31-year-old man, was taken to hospital for mandatory testing,” NSW Police said in a statement.
Police are investigating the circumstances surrounding the crash.