Britain's leading female rider, who won individual bronze and team silver at the 2004 Olympic Games, led three day eventing's most prestigious annual competition from start to finish.
Despite a strong final day challenge from Athens team-mate William Fox-Pitt, Funnell and Primmore's Pride produced a clear round with no time faults in the final day's showjumping to take the title.
Funnell said she was confident of securing victory, even though a single fault would have knocked her off the top spot.
"I knew William would go clear," she said. "And while 'Kiri' hung on my hand a couple of times I don't have to worry too much as he is such a fantastic jumper."
Australia's reigning Olympic champion Andrew Hoy finished third on Master Monarch.
More than 150,000 spectators enjoyed four days of action at Badminton, which takes place on the Gloucestershire estate of the Duke of Beaufort.
The event was first held in 1949 after the 10th Duke was inspired by the three-day event competition at the 1948 London Olympic Games.
The BBC provided live TV coverage throughout the weekend, including the pioneering use of digital technology to cover every single round of the cross country stage.
9 May 2005