He is best known for having managed a number of top clubs in Serie A, and won a scudetto with A.C. Milan in 1999. Among other notable clubs coached by Zaccheroni include Lazio, Inter and Juventus, all as interim coach for part of a season. He won the Asian Cup in 2011 with the Japan National Team. He is also renowned for his unconventional and trademark 3–4–3 tactical system.
Zaccheroni's playing career was cut short by injury, and he became a manager at the relatively young age of 30 with amateurs Cesenatico. He won Serie C2 and Serie C1, the fourth and the third highest football leagues in Italy. His managerial career took off during the Serie A 1997–98 season with Udinese, when he guided them to third place in the league and qualification for the UEFA Cup.
Zaccheroni's results at Udinese attracted the attention of Italian giants A.C. Milan, who appointed him as manager after the San Siro club had endured two miserable seasons. Fellow Udinese key players Oliver Bierhoff and Thomas Helveg also joined him in Milan. Zaccheroni delivered instantly, as Milan won the league in the 1998–99 season, pipping Lazio and Fiorentina to the title. The following season was less successful for Zaccheroni as Milan exited the UEFA Champions League early, and although finishing 3rd in Serie A, they were never really in the running for the title. The 2000–01 season was even worse for Zaccheroni as Milan, again, struggled in the Champions League and failed to beat Deportivo. This led AC Milan chairman Silvio Berlusconi to sack Zaccheroni and replace him with caretaker manager Cesare Maldini in the spring of 2001.
Zaccheroni was without a job for a few months before Lazio came calling, after Dino Zoff had resigned. The Rome-based club had endured a terrible start to the season. He changed things around and managed to bring a sixth-place finish, thus earning Lazio a UEFA Cup place. Zaccheroni was not without his critics, though, as he played Mendieta and Fiore out of position, thus failing to get the best out of them. He was also held responsible by many for the humiliating 5–1 defeat to Roma in the Rome derby that season. Despite Zaccheroni's efforts, he parted company with the Italian giants, to be replaced by Roberto Mancini.
Zaccheroni was again called upon in the mid-season of 2003–04, this time to try to save Internazionale after the departure of coach Héctor Cúper from the club. Despite crashing out of the Champions League after a humiliating 5–1 defeat to Arsenal at the San Siro, he managed to lift Inter to 4th place in Serie A, thus earning them a Champions League place for next season. However, Inter president, Massimo Moratti, was not convinced of Zaccheroni's abilities, and he was again replaced by Roberto Mancini.
After two seasons without a job, he was linked with a move to England in the vacant manager's post at Crystal Palace. These rumors never came to fruition. He did, however, become the new head coach of Torino on September 7, 2006, the 100th anniversary of the team, replacing Gianni De Biasi, fired by chairman Urbano Cairo three days before the start of the new season despite having led the team to instant promotion from Serie B. However, despite a good start, Zaccheroni was not able to bring Torino to the top positions in the league table and even suffered a worrying sequence of six consecutive defeats, which led chairman Cairo to sack him on February 26, 2007, and reinstate De Biasi at the helm of the granata.
On January 29, 2010 he was appointed to replace Ciro Ferrara as head coach of under-crisis Italian club Juventus. He signed a four-month contract. On 14 February 2010, Zaccheroni achieved his first win as a Juventus manager, defeating Genoa 3–2. His first loss in charge of the team arrived two weeks later, a 0–2 home defeat to Palermo.
He also guided Juventus through the newly established UEFA Europa League campaign, after the club failed to qualify to the first knockout round of the UEFA Champions League. In his first game at European level with Juventus, his side defeated 2–1 AFC Ajax in Amsterdam (the return leg then ended 0–0), and then went on to play English opponents Fulham. The first leg ended in a 3–1 win, but in Craven Cottage his side suffered a 4–1 defeat, sending Juventus out of the competition on a 5–4 aggregate scoreline. After a good start, results fell down again, similarly to the way they did during Ferrara's tenure, and Juventus ended the season in seventh place, thus concluding what was remembered as one of the most troubled Serie A seasons for the bianconeri.
On 30 August 2010, it was revealed via an announcement from the Japan Football Association that Zaccheroni would become the new manager of the Japan national football team. However, due to a visa problem, he was not able to take charge in the first two matches against Paraguay (1–0) and Guatemala (2–1), in which former Japan striker and JFA technical director Hiromi Hara took charge. The first match he took charge, Japan had a historic 1–0 win over Argentina.
His first major competition with Japan was the 2011 AFC Asian Cup, hosted in Qatar. He led the team to their record fourth Asian Cup title, winning 1–0 in the final against Australia.
He led Japan to become the first nation to qualify for the World Cup finals in Brazil after their 2014 FIFA World Cup qualifying football match against Australia in Saitama on 4 June 2013. Japan opened their campaign at the World Cup with a 2–1 defeat to Ivory Coast, where they led the match until 64 minutes. In the next match, Japan faced Greece, which ended 0–0. They were eliminated in the group stages after a 4–1 defeat to Colombia and finished fourth with one point. At the end of the tournament, Zaccheroni resigned as the manager of Japan.
On 19 January 2016, Zaccheroni was appointed the new manager of Chinese Super League club Beijing Guoan, on a two-year contract. However, after a dismal start to the season, which saw Guoan pick up just 9 points in their first 9 games of the season, combined with the team scoring just 7 goals in their first nine games, along with growing discontent amongst the fans, Zaccheroni was sacked by the club.As of 20 May 2016
Serie A: 1998–99
AFC Asian Cup: 2011
EAFF East Asian Cup: 2013
Albo Panchina d'Oro (2): 1996–97, 1998–99
Serie A Coach of the Year: 1999