The 17-year-old American broke the previous record of 3:59.15, set by Italian Federica Pellegrini on July 26, 2009 in the era of the now-banned high-tech bodysuits.
Ledecky, whose morning swim of 3:59.89 had already made her the first woman to twice break four minutes in the event, broke through the 3:59 barrier to add the record to her 800m free and 1,500m free world marks.
She's the first woman since US distance great Janet Evans to hold the world records in all three of those events at the same time. Evans did so from 1988 to 2006.
Ledecky, calling her race "pretty close to perfect," was under world record pace at every wall. At the halfway stage she was a whopping 1.71sec under Pellegrini's pace, although by the 300m mark she was just three-tenths under and had to dig deep on the last 100.
"I just put it all out there," Ledecky said. "I tried to make sure I didn't rush the first 100, then after that I could just race."