Harper broke into both film and television in 1993, doing recurring work on the Fox series Married...with Children and making his film debut in the short Confessions of a Dog. He had his first substantial role in a feature in Spike Lee's Get on the Bus (1996), which cast him as a UCLA film student riding a bus to the Million Man March in Washington, D.C. He went on to further demonstrate his versatility in such films as Lee's He Got Game (1998) and Christopher Scott Cherot's Hav Plenty (1997), the latter of which featured him as an egotistical pop-soul singer.

His profile subsequently rose on both the mainstream and independent film circuits, thanks to roles in films ranging from Beloved (1998) to the independent romantic comedy Loving Jezebel (1999) to The Skulls (2000), an entry into the teen thriller/horror genre. Harper also did some of his most acclaimed work in Jordan Walker Pearlman's The Visit (2000), an independent drama in which he starred as a prisoner dying of AIDS