Spacey has not appeared on the screen or on stage since Rapp came forward.
A judge ordered him not to contact his alleged victim, setting another hearing for March 4.
The actor's legal team claims, however, that they believe text messages from the alleged victim and his girlfriend could prove that Spacey did not assault the man, but rather that the interaction was consensual.
Spacey's request was denied by the judge and so he did appear in person to enter his plea.
Upon entering the courtroom, Spacey sat whispering and occasionally chuckling with his attorney, Alan Jackson. The alleged victim was represented by assistant district attorney Michael Giardino.
Mexican actor Roberto Cavazos, who performed in several Old Vic productions, said "it seems that it only took a male under 30 to make Mr Spacey feel free to touch us".
"By reporting the sexual assault, my client is determined an encouraging voice for those victims not yet ready to report being sexually assaulted", the alleged victim's attorney told E!
Spacey is one of dozens of men in the entertainment industry and politics who have been accused of sexual misconduct in the past 10 months, partly as a result of the #MeToo social media movement. Spacey's lawyers wrote that the teen lied about his age, "welcomed" drinks bought by Spacey, left the bar with him to smoke a cigarette and gave Spacey his phone number.
They come more than 13 months after the complaint was filed, the latest chapter in Hollywood's reckoning over sexual assault and harassment that has already seen television icon Bill Cosby jailed and movie mogul Harvey Weinstein indicted.
In court papers, the defense has also targeted Unruh, asserting that she is the "driving force" behind the prosecution of Spacey, who is charged under his real name, Kevin S. Fowler, and not her son.
In 2017, Unruh said at a news conference that Spacey had forced himself on her son.
Kevin Spacey arrives at Nantucket District Court for his arraignment.
Spacey could face up to five years in jail if convicted.
In October 2017, actor Anthony Rapp told BuzzFeed News that Spacey tried to sexually proposition him when he was 14 and Spacey was 26. The man said he fled when Spacey went to the bathroom.
Later that day, the actor released video in which he appeared as his House of Cards character Frank Underwood.