BALTIMORE — A Baltimore judge on Monday ordered the release of Adnan Syed after overturning Mr. Syed’s conviction for the 1999 murder of Hae Min Lee — a case that was chronicled in the hit podcast “Serial,” a true-crime series that transfixed listeners and revolutionized the genre.

At the behest of prosecutors who had uncovered new evidence, the circuit court judge, Melissa Phinn, ordered that Mr. Syed’s conviction be vacated as she approved the release of the now-41-year-old who has spent more than two decades behind bars. There were gasps and applause in the crowded courtroom as the judge announced her decision.

Judge Phinn ruled that the state violated its legal obligation to share evidence that could have bolstered Mr. Syed’s defense. She ordered Mr. Syed to be placed on home detention with GPS location monitoring. The judge also said the state must decide whether to seek a new trial date or dismiss the case within 30 days.

“All right Mr. Syed, you’re free to join your family,” Judge Phinn said as the hearing ended.

Minutes later, Mr. Syed emerged from the courthouse and flashed a small smile as he was shepherded to a waiting SUV through a sea of cameras and a cheering crowd of supporters.

Mr. Syed has always maintained his innocence. His case captured the attention of millions in 2014 when the debut season of “Serial” focused on Lee’s killing and raised doubts about some of the evidence prosecutors had used, inspiring heated debates across dinner tables and water coolers about Mr. Syed’s innocence or guilt.

Last week, prosecutors filed a motion saying that a lengthy investigation conducted with the defense had uncovered new evidence that could undermine the 2000 conviction of Mr. Syed, Lee’s ex-boyfriend.

“I understand how difficult this is, but we need to make sure we hold the correct person accountable,” an assistant state’s attorney, Becky Feldman, told the judge as she described various details from the case that undermine the decades-old conviction, including other suspects, flawed cellphone data, unreliable witness testimony, and a potentially biased detective.

Mr. Syed was serving a life sentence after he was convicted of strangling 18-year-old Lee, whose body was found buried in a Baltimore park.

The investigation “revealed undisclosed and newly-developed information regarding two alternative suspects, as well as unreliable cell phone tower data,” State’s Attorney Marilyn Mosby’s office said in a news release last week. The suspects were known persons at the time of the original investigation, but weren’t properly ruled out nor disclosed to the defense, prosecutors said. They declined to release information about the suspects, due to the ongoing investigation.

Prosecutors said they weren’t asserting that Mr. Syed is innocent, but they lacked confidence “in the integrity of the conviction” and recommended he be released on his own recognizance or bail. The state’s attorney’s office had said if the motion were granted it would effectively put Mr. Syed in a new trial status, vacating his convictions, while the case remained active.

Mr. Syed was led into the crowded courtroom in handcuffs Monday. Wearing a white shirt with a tie, he sat next to his attorney. His mother and other family representatives were in the room, as was Ms. Mosby.

In 2016, a lower court ordered a retrial for Mr. Syed on grounds that his attorney, Cristina Gutierrez, who died in 2004, didn’t contact an alibi witness and provided ineffective counsel.

But after a series of appeals, Maryland’s highest court in 2019 denied a new trial in a 4-3 opinion. The court of appeals agreed with a lower court that Mr. Syed’s legal counsel was deficient in failing to investigate an alibi witness, but it disagreed that the deficiency prejudiced the case. The court said Mr. Syed waived his ineffective counsel claim.

The U.S. Supreme Court declined to review Mr. Syed’s case in 2019.

The true-crime series was the brainchild of longtime radio producer and former Baltimore Sun reporter, Sarah Koenig, who spent more than a year digging into Mr. Syed’s case and reporting her findings in almost real-time in hour-long segments. The 12-episode podcast won a Peabody Award and was transformative in popularizing podcasts for a wide audience.

“Justice is always worth the price paid for its pursuit,” Ms. Mosby said in a news conference after the hearing.