On Monday, Judge Addison Howard granted a motion of acquittal for Michael Johnson because of insufficient evidence.
Russell Barnes, Phylicia Barnes' father, said the ruling was heartbreaking. "I feel like I got run over by a train," he said.
The body of the 16-year-old Barnes was found floating in a Maryland river
in spring 2011. Authorities said she was found without clothes and with no "overt" signs of wounds or injuries.
The teen had been visiting her half-sister in Baltimore. She said she was going out to get something to eat and maybe a haircut when she left the residence.
About a year after her body was found, police arrested Johnson, the half-sister's ex-boyfriend.
Johnson was convicted of second degree murder in January 2013.
But his attorneys successfully argued that he should have a new trial because the prosecution withheld evidence about a witness who linked Johnson to the killing, according to the judge's order that summarized the case.
Last month, the second trial ended in a mistrial because the jury was allowed to hear information in recordings that should have been redacted, the court order stated.
Defense lawyers filed a motion for acquittal.
The judge's order said there was plenty of circumstantial evidence against Johnson, including that he was the last person known to see Barnes and that a witness watched him sweating as he carried an object in a tote down the apartment stairs on the day she disappeared.
However, the judge wrote, "there was insufficient evidence when taken as a whole" to convict Johnson on a charge of second-degree murder.
Prosecutors tweeted a statement saying they disagree with the judge's decision and will appeal the ruling.
Defense lawyer Kay Beehler issued a statement saying, "This case was a tragedy for everyone in the Barnes and Johnson families. Ms. Barnes was a lovely, vibrant young woman. However, Mr. Johnson has maintained his innocence from Day One of this entire case, and we are very thankful that justice was done. "
Johnson left jail and was met by reporters on the street. "It feels great to be out," he said.
Russell Barnes said he'll keep working to put Johnson behind bars.
"We just can't let this go," he said. "We have to see justice for Phylicia. We're just going to pursue ... the same gentlemen, a child killer who's on the streets of Baltimore."