He was originally selected by the NBA's Chicago Bulls in 1990. He continued to play in Europe however, until finally reporting to the Bulls in 1993. At that time, however, the team had just finished its three-peat and had lost Michael Jordan to retirement.
The 6' 11" Kukoč came off the bench in 1993-94 behind small forward Scottie Pippen and power forward Horace Grant, though he could play shooting guard and center as well. Kukoč put up a solid rookie campaign, averaging double-digit scoring and earning a berth on the all-rookie second team. After Grant left in the offseason, Kukoč moved into the starting lineup and finished the 1994-95 season second on the Bulls in scoring, rebounds and assists behind Scottie Pippen.
For the 1995-96 season, although Kukoč was clearly improving rapidly, he was again coming off the bench. Michael Jordan had returned, and the Bulls acquired rampant rebounder Dennis Rodman in the offseason. With Pippen still at small forward, coach Phil Jackson saw it best to have Kukoč spark games when he came in with bursts of scoring. Toni was third on the team in scoring behind Jordan and Pippen, and was rewarded for his efforts with the sixth man of the year award. He also assisted the Bulls to a 25 game turnaround and the best record in league history at 72-10, as well as the fourth championship in team history.
In 1997 and 1998 Kukoč again came off the bench as sixth man as the Bulls won their fifth and sixth world championships, with the Croatian Sensation placing third on the team in scoring each year.
In the summer of 1998 the team was callously dismembered, and Kukoč found himself the lone marquee player left. He responded for the 1998-99 season by leading the Bulls in scoring, rebounding and assists. During the 1999-2000 season he was traded to Philadelphia as Chicago continued their rebuilding scheme, and soon moved to Atlanta before stopping at the Bucks in Milwaukee.