Methods, systems, and media for presenting user comments containing timed references in synchronization with a media content item are provided. In some embodiments, a method for presenting user comments during media playback that includes: obtaining a plurality of comments associated with a media content item; determining a subset of comments from the plurality of comments that contains at least one of a plurality of timed references to the media content item; determining a series of time windows, wherein each time window in the series of time windows corresponds to a segment of the media content item; associating one or more comments from the subset of comments with a time window from the series of time windows, wherein the time window contains a time referenced in a comment; receiving a request to receive comments that are synchronized with playback of the media content item; and, in response to receiving the request to receive comments that are synchronized with playback of the media content item, causing a first comment associated with a first time window to be presented concurrently with a first portion of the media content item that corresponds with the first time window and a second comment associated with a second time window to be presented concurrently with a second portion of the media content item that corresponds with the second time window.