On 7 July 1999, in Roma, Ngeny was second to Hicham El Guerrouj when the latter set the world record (3:43.13) for the mile run.

Ngeny stayed close to El Guerrouj down the stretch to finish at 3:43.40, still the second-fastest mile ever run as of 2023[update], and almost a full second inside the old world record (3:44.39) of Noureddine Morceli.

On 11 August 2000, Ngeny finished second to El Guerrouj (3:27.21) in the 1500 m at the Weltklasse Zürich meet in a time of 3:28.12, making him the Kenyan record holder and third-fastest ever in the event.

El Guerrouj settled for silver in 3:32.32 and Ngeny's compatriot Bernard Lagat, another Kenyan runner at that time, later a US citizen, took bronze in 3:32.44.

He posted career bests of 1:44.49 for 800 m (28 July 2000 in Oslo) and 3:28.12 for 1500 m (at the Weltklasse Zürich on 11 August 2000), en route to his Olympic triumph (29 September 2000).

Ngeny was dropped from the Kenyan team for the 2001 World Championships in Edmonton after defying instructions from the national federation to return home from Britain where he trained.

He competed sparsely in 2003 and 2004 recording a best time of 3:33.38 but failing in his attempt to qualify for the Kenyan Olympic team, and was not able to defend his title in Athens.