Methods, systems, and media for detecting and transforming rotated video content items are provided. The method comprises: receiving a video having a plurality of frames, wherein the video is associated with a first fingerprint; determining a rotation value associated with at least a portion of the plurality of frames to obtain a plurality of rotation values; determining an overall rotation value associated with the video based on a portion of the plurality of rotation values; determining whether at least one additional fingerprint of the video should be generated based on the overall rotation value; in response to determining that the at least one additional fingerprint of the video should be generated based on the overall rotation value, selecting a rotation transform based on the overall rotation value that rotates the plurality of frames of the video to an initial rotation position; applying the rotation transform to at least a portion of the plurality of frames of the video; generating a second fingerprint that represents the transformed video; and comparing the second fingerprint of the transformed video to a plurality of fingerprints associated with reference videos to determine whether the video corresponding to the transformed video matches one of the reference videos.