He played for Jugoplastika Split and won a championship with the team three times. No other team has achieved this success of the legendary Jugoplastika team and won the European crown three times in a row. Afterwards he played for Benetton Treviso, winning the title of European Player of the Year three times. Though a young player he was considered one of the best players in the game. One of his nicknames was "white magic". Sometimes he was referred to as "the spider from Split" or "the Croatian Sensation". But his most fitting nickname was and is "the waiter", since he passed the ball around like few players ever have. He was also on teams that won the FIBA World Junior Championship (1987 for Yugoslavia), two Olympic silver medals (1988 for Yugoslavia and 1992 for Croatia), and the FIBA World Championship (1990 for Yugoslavia).

Having been drafted by the NBA's Chicago Bulls in 1990, he 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.

The 6' 11" (2.11 m) Kukoč came off the bench in 1993-94 behind small forward Scottie Pippen and power forward Horace Grant, though Kukoč 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 Pippen.

In the 1995-96 season, although Kukoč was improving rapidly, he was again coming off the bench. Michael Jordan had returned, and the Bulls had 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 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 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 NBA titles. Once again, he was the team's third-leading scorer.

In early 1999, the team was disbanded, and Kukoč found himself the lone marquee player left. In the lockout-shortened 1998-99 season, he led the team in scoring, rebounding, and assists. During the 1999-2000 season as Chicago continued their rebuilding scheme, Kukoč was traded to the Philadelphia 76ers for whom he played briefly before he was soon traded again to the Atlanta Hawks. After a short stint with the Hawks, he finally found himself in a more suitable fit with the Milwaukee Bucks via a third trade.