The career criminal accused of fatally shooting the 12-year-old son of a retired NYPD cop pleaded not guilty Thursday — as the boy’s heartbroken mother fought back tears just feet away in a Bronx courtroom.

William Ferrer, 45, clad in beige jail scrubs, entered the plea in Bronx Supreme Court in the July 25 stray-bullet killing of little Jacob Freytes, who was caught in the crossfire outside a Mount Eden bodega.

Jacob’s mom, Migdalia Martinez, dabbed her eyes with a tissue as she watched Ferrer in court for the first time, surrounded by about a dozen family members.

William Ferrer, 45, clad in beige jail scrubs, pleaded not guilty in Bronx Supreme Court in the July 25 stray-bullet killing of 12-year-old Jacob Freytes, who was caught in the crossfire outside a Mount Eden bodega. Tomas Gaston for NY Post

“I just wanted him to see how I felt, what he left me with. I feel like a shell. I carry a burden,” the devastated mom told The Post. “I don’t feel like I deserve this.”

Martinez wore a T-shirt emblazoned with photos of herself and her slain son.

Ferrer, who has at least a half-dozen prior arrests dating back to 1999, is accused of opening fire during a street dispute outside Wanda Deli Grocery on Elliott Place near the Grand Concourse.

Jacob, the son of retired NYPD Detective Sgt. Jesus Freytes, had biked to the store to buy a ball when gunfire erupted, authorities have said.

Heartbreaking surveillance footage showed the youngster clutching his chest and staggering back into the bodega after he was struck. Two men were also wounded in the gunfire.

Before Thursday’s hearing, Bronx Supreme Court Justice Alvin Yearwood ruled that The Post could photograph Ferrer inside the courtroom, rejecting a defense bid to keep cameras away from the accused killer.

Freytes mother, Migdalia Martinez, wiped her eyes in the courtroom along with several family members after seeing Ferrer in court for the first time. Facbook/El Nene Kai

“This was an incident that was allegedly on video,” Yearwood said. “Even I, as a Bronx resident, saw the video.”

“I don’t know that there can really be any prejudice by photographing the defendant at the proceeding,” the judge continued.

“Additionally, this court believes in the public’s right to know. You open the doors wide, you allow the public to see what’s happening, and that will help to provide confidence in the system, that we are not doing things in the dark.”

Martinez told The Post while wearing a shirt with photos of herself and her slain son, “I just wanted him to see how I felt, what he left me with. I feel like a shell. I carry a burden.” TOMAS E. GASTON

Yearwood also addressed Jacob’s grieving relatives directly from the bench, warning them that the case could drag well into next year.

“One of the things I try to explain is that, look, the case is in the court system. It’s not going to be resolved tomorrow,” Yearwood told the family seated in the gallery.

“You’re welcome to come to every single court date, but understand you’re not getting a trial before the end of this year because unfortunately we have a lot of cases that we have to work through.”

Ferrer, a career criminal with arrests going back as far as 1999, allegedly fired multiple shots outside Wanda Deli Grocery near Grand Concourse, resulting in the youngster’s death along with two other men being wounded during the shooting. Kevin C. Downs for NY Post

Outside court, Martinez said she had previously seen Ferrer on the streets — but that laying eyes on the man accused of taking her son’s life was entirely different.

“Whether I’ve seen him before or not, it’s a lot different when you see them after they committed something like that to someone you love,” she said.

Martinez blasted what she sees as Ferrer’s effort to delay facing the consequences of her son’s death.

“He’s trying to buy time. The system is just messed up. This is just a mockery to him,” she said.

“From his point of view it was an accident, but hey, as long as I don’t do life it’s fine.”

Ferrer faces murder, attempted murder, manslaughter, assault and weapons charges in the shooting. He is due back in court Nov. 17.

Yearwood ordered him to remain held without bail.