It was first held as the ICC KnockOut Tournament in 1998, and since then, it has taken place about every four years. In 2002, the trophy was renamed the Champions Trophy. The Bangabandhu National Stadium in Dhaka, Bangladesh, hosted each game during the 1998 tournament. South Africa won the competition by defeating West Indies in the championship match. With 221 runs scored, Philo Wallace of the West Indies was the competition's top run scorer. The Gymkhana Club Ground in Nairobi, Kenya, served as the site of every game during the 2000 tournament. The competition had participation from all test-playing nations, with the finals including Kenya, India, Sri Lanka, the West Indies, Bangladesh, and England. New Zealand won the competition by defeating India in the championship match. In this competition, Sourav Ganguly, the captain of India, scored the most runs with 348. The top wicket-taker was Venkatesh Prasad. This was New Zealand's first ICC victory. Also, until 2021, it remained their only ICC trophy.

The 10 ICC Test-playing nations, plus the recently admitted full member Bangladesh, Kenya (ODI status), and the 2001 ICC Trophy champions Netherlands, competed in the 2002 ICC Champions Trophy, which was held in Sri Lanka. Rain twice caused the final between India and Sri Lanka to be canceled, leaving no conclusion. Before the rain prompted an interruption, Sri Lanka batted 50 overs before India played two overs. India played 8 overs the following day, while Sri Lanka again bowled 50 overs. India & Sri Lanka were recognized as equal champions in the end. There was no outcome despite the 110 overs played by the sides. Muralitharan (10) had the most wickets in the competition, and Virender Sehwag (271) had the most runs.

The ICC CT 2004 was played in England, and the participating nations featured the 10 ICC Test nations, Kenya (who has ODI status), and the United States, who were playing in their first One Day International after qualifying by winning the most recent ICC Six Nations Challenge. Teams losing just one game in the group phase were eliminated from the competition, which was more akin to a knockout series. The top two teams from each of the four groups—made up of the 12 teams played in the semi-finals. ENG overcame AUS in the first semi-final to get to their fourth ICC tournament final. In the second semi-final, PAK fell to WI in a low-scoring contest. With the aid of wicketkeeper C Browne & tailender Ian Bradshaw, the WI squad led by Lara prevailed in the decisive game.

The final of the 2006 ICC Champions Trophy took place on November 5, 2006, in India. The format was changed. The top 6 teams in the ICC ODI Championship on 1 April 2006, together with two teams selected from each of the other four Test-playing nations—Sri Lanka, West Indies, Bangladesh, and Zimbabwe—through a pre-tournament round robin qualifying round—were participating in the group round. Bangladesh and Zimbabwe did not cut, while West Indies & Sri Lanka did.

In a round-robin play, the 8 teams were then placed into two teams of four. South Africa & New Zealand qualified for the semifinals from Group B, while Australia and the West Indies did so from Group A. Australia and West Indies defeated New Zealand & South Africa, respectively, to go to the final. Australia won the trophy for the very first time after defeating West Indies by an 8-wicket margin in the final. The competition was held in Mohali, Ahmedabad, Mumbai, and Jaipur.

Pakistan was chosen by the ICC in 2006 to host the 2008 ICC Champions Trophy. The 2008 ICC Champions Trophy in Pakistan has been moved to October 2009, it was reported on August 24, 2008, since numerous nations were hesitant to travel there because of cricket security concerns. There was considerable doubt that it would happen in 2009 because of the hectic international calendar surrounding that date and uncertainties regarding how the security environment would have altered by then.

On March 16, 2009, it was announced that South Africa should host the 2009 ICC Champions Trophy in place of Pakistan. The 2009 ICC Champions Trophy will be held in South Africa from September 24, 2009, to October 5, 2009, according to a statement made on April 2, 2009, by Cricket South Africa. In the first semi-final, Australia defeated England by nine wickets, and in the second, New Zealand defeated Pakistan by five wickets, setting up a match in which Australia defeated New Zealand by six wickets in 45.2 overs.

The 2013 Champions Trophy was held in England and Wales. The only nation to host the Champions Trophy twice was England. At Edgbaston, India defeated England by 5 runs to win their second championship; their previous trophy, in 2002, was split with Sri Lanka because the final was washed out.

The ICC Champions Trophy was held in 2017 in England & Wales. England became the only nation to host the Champions Trophy three times, and England and Wales, which also hosted the 2013 edition, became the only nations to host the ICC Champions Trophy back-to-back. The West Indies were replaced by Bangladesh in the ICC ODI Team Rankings on the cutoff date after they ranked ninth and outside the top eight. For the first time since 2006, Bangladesh qualified for the ICC Champions Trophy, but the West Indies did not.

Arch-rivals for the very first time since 2007, India and Pakistan squared off in a tournament final. The match took place in London's The Oval. It was Pakistan's first participation in a Champions Trophy final and India's fourth. Pakistan easily defeated India by 180 runs, outperforming them in all three categories (batting, bowling, and fielding). The lowest-ranked squad in the tournament, Pakistan, won the Champions Trophy for the first time and became the eighth country to do so.