The defense argued that the girl slipped and fell 120 feet to her death.
However, for the second time, prosecutors find themselves facing a hung jury.
Brown was charged with first-degree murder for the death of Lauren Sarene Key in November 2000 in Rancho Palos Verdes. The charge included the special circumstance allegations of murder for financial gain and murder while lying in wait, and carried a potential life prison sentence without the possibility of parole.
After three weeks of deliberating, jurors announced Monday they were deadlocked on Brown's guilt, resulting in a second mistrial in this case.
"The little girl was killed, we feel, but it was a split decision," said juror Stephan Burkett.
Jury foreman Mark Dreskan said even though jurors agreed that Brown was guilty of something, they split right down the middle on second-degree murder and involuntary manslaughter. He said jurors struggled over whether Brown deliberately killed Lauren or was a careless father who let his daughter roam near a harrowing precipice.
"Nobody thought he was not guilty," Dreskin said. "It was primarily a decision between if there was intent or not, not the method of the fall, the mechanism of the fall, as important as those things were, it wasn't the final sticking point. It was this question of intent."
Brown's defense attorney, Pat Harris blasted prosecutors for twice trying to prove first-degree murder and twice being rebuffed by juries.
"From the very beginning, we've talked about the fact that we would have accepted an involuntary manslaughter plea, but again, an involuntary manslaughter implies totally that there is no fault, it's an accident, and that's what this case has been from the beginning," Harris said.
In the meantime, Brown is remains in custody. He has been jailed for the past six years.
Brown was tried three years ago, but a mistrial was declared after a jury deadlocked on the severity of the crime.
The district attorney's office has declined to say whether Brown would be retried. He's due back in court at the end of October.
The Associated Press contributed to this report.