Syed is serving a life sentence after he was convicted in 2000 of strangling Ms Lee, his high school classmate and ex-girlfriend, before burying her body in Baltimore's Leakin Park.
His lawyers had argued that his trial lawyer's failure to investigate an alibi witness violated his right to competent legal representation.
However the highest court in the US has stood by the decision made by the Maryland court of appeals, which reinstated Syed's conviction for the murder of the 17-year-old in March. A filing from the court listed Syed's case among more than 100 others where justices had elected to agree with the initial ruling.
The decision means Justices sided with the close 4-3 decision agreed by Maryland judges, who decided there had been a “deficient performance” from his defence attorney Cristina Gutierrez, but still found the evidence against Syed pointed towards guilty.
Lawyers for Syed have argued that the case against him was tarnished by a flawed legal process - and that the decision not to call forward witness Asia McClain meant he had not received proper legal representation from Ms Gutierrez.
In a petition to the Supreme Court, his legal representation said: “Few of Syed’s classmates could remember Syed’s activities right after school on the day Lee was killed.
“Indeed, only two teenagers could testify on that issue: The first—Jay Wilds—said that Syed showed him Lee’s body in the trunk of a car shortly after school. The second—Asia McClain—said that she talked to Syed at the library adjacent to the high school between 2:15 and 2:35 pm that day, and that others could corroborate her story.
“In a normal case, it would be left to the jury to determine who is credible: Wilds or McClain. In this case, however, the jury never heard McClain’s testimony."
Arguing the failure to call on Ms McClain breached Syed's right to a fair trial, lawyers for the now-40 year old added: “The facts of this case are eye-catching - One high school student murdered and another sentenced to life in prison. A prosecution witness with an inconsistent story and an alibi witness who never testified at trial.
“Syed’s case has inspired podcasts, a documentary, and countless news articles. This petition, however, is about a straightforward legal issue.”
In its debut 2014 season, the "Serial" podcast hosted by Sarah Koenig shined a spotlight on the case that led to renewed court proceedings. The murder was also the focus of the HBO miniseries The Case Against Adnan Syed.