Daniel Penny was found not guilty in the criminal case, but he now faces a civil suit from Jordan Neely’s father, who was absent most of his son’s life.

Andre Zachary filed his wrongful death claim against Penny just days before a Manhattan jury acquitted the Marine vet of negligent homicide charges in the highly charged encounter last year, and the suit carries a new set of challenges, legal experts told The Post.

“He has that elephant in the room to address, first as a personal and second as a legal matter — what was he thinking to apply so much force that the man died?” said attorney Lanny Davis, a former adviser to ex-presidents Bill Clinton and George W. Bush. “He has not explained because, as a criminal defendant, he didn’t take the stand to explain why he exerted such force that the man died.”

The burden of proof from criminal cases to civil cases changes the playing field, Davis said.

“From reasonable doubt to more likely than not. It’s very important that he get his version of the truth out.”

Filed Dec. 4 during Penny’s criminal trial, Zachary’s complaint seeks an unspecified amount in damages, accusing the subway vigilante of fatally assaulting Neely on May 1, 2023.

A jury of six Manhattan residents will decide the outcome of the civil case if it goes to trial, with five of the six required to decide if Penny “negligently” caused Neely’s death. Penny, who did not take the stand at his criminal trial, will have to sit down for a deposition that will likely be videotaped.

He could also be called on to take the stand if the case goes to trial.

Growing up, Neely bounced around different homes in the foster care system after his mother died in 2007 when he was 14 years old.

The troubled young man didn’t move in with Zachary until he was 18 — and their time living together was marred by financial strife.

The father and son would argue after Zachary asked Neely to share proceeds he earned from his performances as a Michael Jackson impersonator and he refused, according to a profile on Neely by New York magazine.

During those fights, Zachary would take away Neely’s house keys, Neely’s friend Dwayne Blizzard reportedly said. Zachary denied that accusation to the outlet.

Neely and his father grew estranged during the later part of the 30-year-old’s life as the Neely’s struggled to scrap by, according to a New York Times report.

Zachary’s lawyer, Donte Mills, said Tuesday that he’s not worried in the wake of Penny’s acquittal.

“We don’t believe the criminal result will have any impact in our case, because it’s a different standard,” Mills said. “Did he hold that chokehold for too long when people were telling him to let go? Should he have let go? That’s what it’s going to come down to.

“And I think Manhattanites will understand that, and will come back with the verdict that says they do.”

One prominent attorney, Manhattan-based civil litigator Rich Schoenstein, said Penny’s acquittal of criminally negligent homicide charges could carry some weight if he goes before a civil jury.

“A conviction would have been very problematic in the context of civil litigation because when you lose an argument in one court, you are supposed to be bound by that in other courts,” Schoenstein said.

But he said it doesn’t mean it’ll be a slam dunk for Penny.

“The acquittal does not bar the civil claim at all,” Schoenstein said. “With a new jury and the burden of proof reduced, as the defense you can’t make any assumptions.”

One cautionary tale for Penny is the case of onetime NFL star OJ Simpson, who was acquitted of killing his estranged wife Nicole Brown Simpson and her pal Ronald Godlman at a circus-like trial in 1994.

But three years later a California civil jury ordered him to pay the victims families more than $33 million.

“OJ is a good example of a case where you couldn’t get a criminal conviction but the families of the victim were able to hold the defendant somewhat accountable in civil court,” Schoenstein said.

John Q. Kelly, who represented the Nicole Brown Simpson’s estate, said Tuesday that Penny could likewise face problems at a civil trial despite his criminal acquittal.

“He can’t assume that jurors who have heard about the case would agree with the acquittal,” Kelly told The Post. “There might be jurors who think he was trying to go ‘Rambo,’ that he knew what he was doing, and that he used excessive force.”

However, he said the acquittal could also have a positive “PR aspect” for Penny.

“But it will be made very clear and very quickly that a civil case is totally different,” Kelly added.

In a joint statement, Penny’s lawyers, Tom Kenniff and Steven Raiser, said they “will defend any civil suit with the same vigor with which we defended against his unjust criminal prosecution.  

“Once again, there will be no compromise,” the statement said.