Smith walked into Jackson Baptist Memorial Church alongside rapper Jermaine Dupri, who discovered the the 1990s teen duo, at an Atlanta mall.
The 34-year-old Kelly was found dead May 1 of a suspected drug overdose. His mother and uncle told authorities Kelly had a history of drug abuse and experienced similar episodes in the past, according to a police report.
Two members of the band Xscape, sisters LaTocha and Tamika Scott, arrived together for Kelly's funeral.
"He just wanted to smile. That's all he wanted," Tamika Scott said. "He was known to be a happy person."
Rapper Da Brat tried to speak to reporters when she arrived but stopped when she got choked up and went on into the church.
Kris Kross was introduced to the music world in 1992 by music producer Dupri after he discovered the pair at Greenbriar Mall in southwest Atlanta. Kelly was known as "Mac Daddy" and Smith was known as "Daddy Mac."
The duo wore their clothes backward as a gimmick, but they won over fans with their raps.
Their first, and by far most successful song, was "Jump." The hit, off their multiplatinum 1992 debut album "Totally Krossed Out," featured the two trading verses and rapping the refrain, the song's title. The duo had surprising maturity in their rap delivery, though the song was written by Dupri. It would become a No. 1 smash in the United States and globally, and one of the most popular of that year.