The music video for "Whole Again" was filmed on a very small budget due to the commercial failure of previous single "Follow Me". It features the girls singing in front of a plain white background. The original version of the video includes Kerry Katona, who had left the group just before the song's release. Much of the video was subsequently reshot to feature new member Jenny Frost.
As a result of the single's huge success in many international markets, a second music video was filmed for the U.S. release with a much larger budget. This version features the three girls walking through the streets in Downtown Los Angeles and walking out into the countryside, gradually picking up more people along the way. The video ends with the camera zooming out on the field for Atomic Kitten's old logo is invisible in a shape of a kitten. The U.S. single release never materialised in the wake of the September 11 attacks, but the video can often be seen on British music television channels.