Hernandez firmly answered "not guilty" to six charges, including murder and weapons and ammunition possession charges.
His attorneys agreed ahead of the hearing that Hernandez, 23, will continue to be held without bail, but reserved the right to request bail later. The next court hearing was set for Oct. 9.
Defence attorney Charles Rankin said outside the courthouse that Hernandez's legal team is confident the ex-Patriot will be exonerated during a trial. "Not one shred of evidence has been presented yet," he said.
The arraignment "is like the opening kickoff," Rankin said. And, he encouraged people to keep an open mind and let the lawyers and the justice system do their work.
Bristol District Attorney Samuel Sutter said, in fact, a "tremendous amount" of evidence has already been presented. He cited 500 pages of documents released to the press and public, including search and arrest warrants, affidavits and photographs taken from a surveillance system at Hernandez's home.
"I think that evidence speaks for itself," he said.
Sutter said he hopes the case will go to trial within a year but that it can sometimes take two years or more.
A Massachusetts grand jury last month returned the indictment against Hernandez in the death of Odin Lloyd, a 27-year-old semi-professional football player from Boston who was dating the sister of Hernandez's girlfriend.
Hernandez was arrested in June and pleaded not guilty to murder and weapons charges in district court. The indictment moved the case to superior court, where jury trials in murder cases are held.
Hernandez, who was cut from the Patriots within hours of his arrest, has been held at a county jail without bail.
Prosecutors say the former NFL star orchestrated Lloyd's killing because he was upset at Lloyd for talking to some people with whom Hernandez had problems at a nightclub a few days earlier.
Defence attorneys say the evidence is circumstantial and that the state's case won't hold up.
More than a dozen members of Lloyd's family attended Friday's hearing, most of them wearing purple. Among them was Ursula Ward, the mother of Odin Lloyd, who had tears streaming down her cheeks at one point during the hearing.
Hernandez's girlfriend, Shayanna Jenkins, and his mother, were seated on the opposite side of the courtroom.
Some people who appeared to be fans of Hernandez gathered outside the courthouse, including one woman with a "Team Aaron" shirt bearing his old jersey number.
Two other men who prosecutors say were with Hernandez when Lloyd was killed are also facing charges. Ernest Wallace was indicted on a charge of accessory to murder after the fact. He earlier pleaded not guilty to the same charge in district court and was ordered held on $500,000 bail.
Carlos Ortiz pleaded not guilty to a firearms charge and is being held without bail. He has not been indicted.
Lloyd's body was found by a jogger on June 17 in an industrial park in North Attleborough, about a mile from Hernandez's home. Authorities say Lloyd was killed with a .45-calibre Glock, which they have said hasn't been recovered. But prosecutors say they have video footage of Hernandez at his home holding what appears to be a Glock, in the hours before and just after the killing.
Prosecutors have not identified the triggerman, but according to court documents, Ortiz told police Wallace said it was Hernandez.
Hernandez's cousin, Tanya Singleton, also was indicted on a criminal contempt charge after prosecutors say she refused to testify before the grand jury hearing evidence in the case, even after they offered her immunity. Her attorney has agreed she be held without bail.
Hernandez is also connected to the investigation of a 2012 double homicide near a Boston nightclub. While probing Lloyd's death, police found an SUV, sought in the earlier killing, at the home of Hernandez's uncle in Bristol, Conn., the former football player's hometown. It had been rented in Hernandez's name.