Kipketer was born in Kapchemoiywo, Kenya, into the Kalenjin tribe.
As a teenager, he was first noticed by 1968 and 1972 Olympic champion Kip Keino. Keino suggested Kipketer attend the Catholic St. Patrick’s High School in Iten that was famous for bringing up young runners.
In 1990, Kipketer travelled to Denmark as a foreign exchange student, studying electronic engineering at the Copenhagen University. He liked Denmark so much that he applied for Danish citizenship. Kipketer competed for Denmark in the 1995 World Championships. It was there that he claimed his first World Championship title in the 800 metres.
However, Kipketer was not a full citizen, and in 1996 the International Olympic Committee disallowed him from competing for Denmark in the Olympic Games in Atlanta, USA. Despite his absence from the Olympics, there was no doubt that Kipketer was the strongest 800 m runner in the world that year. He remained undefeated throughout 1996 and came close to breaking the world record several times, setting a new personal best of 1:41.83 in Rieti at the end of the season.
In 1997 Kipketer was at the peak of his career. In March he won the 800 m gold at the Indoor World Championships in Paris, France. In fact, he broke the indoor world record time in the heats by nearly a second, beating Paul Ereng’s WR 1:44.84 with his 1:43.96. Then in the final he took yet another second off the world record with a scintillating 1:42.67. On 7 July he tied Sebastian Coe’s world record (1:41.73) for the 800 metres at a meeting in Stockholm, Sweden. Coe’s record had stood for sixteen years. He went on to break the record twice that year, the first time being in Zurich, Switzerland at the Weltklasse GP on 13 August when he ran 1:41.24. (His was one of three world records to fall in a 70 minute stretch at this remarkable meet, the other two being the 5,000 meter record to Haile Gebrselassie and the 3,000 meter steeplechase to Wilson Boit Kipketer.) Nine days later, on 24 August, he improved the world record to 1:41.11 at the Grand Prix meet in Cologne, Germany. On 8 August, in the 1997 World Championships in Athletics at the Olympic Stadium, Athens, Greece, he led the race from start to finish, blazing the first 200 meters in 23.47 seconds, and successfully defended the World Championship title he had won in 1995. He was voted Track & Field Athlete of the Year by Track and Field News Magazine.
The following season, Kipketer contracted malaria and at first intended not to race at all. Eventually, he participated in the European Championships in Budapest but made physical contact with the eventual winner Nils Schumann on the final straight and did not win a medal. He came back in 1999 by finishing second at the Indoor World Championships and bettering that with a gold medal at the World Championship in Seville, Spain. As in 1997, Kipketer was undefeated in 1999, winning all 10 outdoor races and finishing the year ranked number one in the world in the 800m by Track & Field News magazine.
In 2000, he broke the world indoor record in the 1000 metres by running a 2:14.96. In the 2000 Summer Olympics in Sydney, Australia, Kipketer took silver in a tactical, closely contested 800 metres race.
In 2002, Kipketer won the gold medal at the European Championships in Munich, defeating the reigning world champion, Andre Bucher and 2000 Olympic champion, Nils Schumann. He also won 8 of the 9 races he contested, had the fastest 800 metre time in the world (1:42.32), and ranked number one in the world for 800 metres for a record sixth time (one more than Mal Whitfield).
Despite fighting injuries, Kipketer continued to compete through the 2003 season gaining a silver medal at the Indoor World Championships at the National Indoor Arena, Birmingham, England but only managing fourth place at the World Championships later that year. In the 2004 Summer Olympics in Athens, Greece Kipketer took a bronze medal in the 800 metres.
He married his Danish girlfriend Pernille in 2000.
He announced his retirement from competitive athletics in August 2005.