Chicago Bulls
After being drafted by the NBA's Chicago Bulls in 1990, Kukoč continued to play in Europe, until finally reporting to the Bulls in 1993, when the team had just finished its first three-peat and had lost Michael Jordan to retirement. Although disappointed that he could not play with Jordan, Kukoč made his NBA debut on November 5, 1993.
The 6 ft 11 in (2.11 m) Kukoč came off the bench in 1993–94 behind small forward Scottie Pippen and power forward Horace Grant. On January 21, 1994, in a game against the Indiana Pacers, Reggie Miller made a mid-range jumper with 0.8 seconds remaining to give the Pacers a 95–93 lead. Scottie Pippen inbounded the ball to Kukoc, who hit a three-point jumper at the buzzer to give the Bulls the win, 96–95. Kukoč put up a solid rookie season, averaging double-digit scoring and earning a berth on the NBA All-Rookie Second Team.
On May 13, 1994, at the end of Game 3 of the Eastern Conference Semifinals, the Bulls and the New York Knicks were tied at 102 with 1.8 seconds left. Bulls coach Phil Jackson designed the last play for Kukoč, with Scottie Pippen charged with inbounding the basketball. Pippen was so angered by Jackson's decision to not let him take the potential game-winner that he refused to leave the bench and re-enter the game when the timeout was over. Kukoč did hit the game-winner, a 23-foot fadeaway jumper at the buzzer, though the Bulls eventually lost the series in seven games.
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 Pippen. Furthermore, Michael Jordan would return to the Bulls in March, fulfilling Kukoč's wish to play alongside him.
For the 1995–96 season, the Bulls were bolstered by both Jordan's return to full form and the offseason acquisition of exceptional rebounder Dennis Rodman. With Pippen still at small forward, coach Phil Jackson saw it best to have Kukoč continue to be a bench player. Kukoč was third on the team in scoring (behind Jordan and Pippen) and was rewarded for his efforts with the NBA Sixth Man of the Year Award. He also assisted the Bulls to a 25-game turnaround and the best record in league history at the time at 72–10 (later surpassed by the 2015–16 Golden State Warriors), as well as the fourth championship in team history. Kukoč was the 4th and is currently the last player to win the NBA Sixth Man of the Year Award and the NBA title in the same year having joined Kevin McHale, Bill Walton, and Bobby Jones in accomplishing that feat.
In 1997 NBA Finals, the Bulls defeated the Utah Jazz in six games, during which at the end of Game 6, Kukoč received the ball from Scottie Pippen and sealed the victory with a dunk to make the score 90–86 with just 0.6 seconds left. A year later, the Bulls defeated the Jazz again in the 1998 NBA Finals. In the 1997 NBA Finals, Kukoč came off the bench as the sixth man and was the team's leading scorer off the bench. By the 1998 postseason, however, Kukoč had moved into the starting lineup, starting all six games of the 1998 NBA Finals.