The video for "Just like a Pill" was directed by Francis Lawrence. The video for the song is considerably different from Pink's previous videos. "Get the Party Started" and "Don't Let Me Get Me" were lighter in nature than the dark atmosphere which is reflected in the video for "Just like a Pill", an example of which is the fact that Pink can be seen throughout the whole video wearing black outfits. In the first scene, Pink lies on the floor. In the chorus she sings in front of her band. She is also featured in another scene with white rabbits around her in a room, and in another scene, she is seen with an elephant. There are also scenes with Pink singing in front of and amongst various people. In the latter half of the video, she runs in a hall whilst lip-synching the song, before disappearing into a bright doorway at the conclusion of the video.

In the video, Pink is seen sitting in front of an elephant. After the elephant had been on the set, she saw the abuse and captivity the animal was in. "Pink learned about the abuse of captive elephants when a trainer brought one onto the set of her 'Just like a Pill' video. She could see that something was wrong and she called us to learn more about the issue. Now, Pink would like to see circuses pack their trunks", according to PETA spokesman Dan Mathews