In keeping with the musical theme of RahXephon, episodes are called "movements" and each volume of DVD is called an "orchestration". Each episode has a title screen that provides an English title for that episode, which generally does not correspond to a translation from the Japanese title. In addition to the 26 regular episodes, one recap episode was aired and one episode was released as an (OVA). These are placed in the list according to the series chronology.
The original air dates are schedule dates; these are calendar dates until the April series break, when Fuji Television moved RahXephon from Monday afternoons into a Tuesday late night anime block. Episodes 10 through 26 started at 25:55, which is at 1:55 a.m. Wednesday. This means that the calendar dates of the first and last episode airings are 21 January 2002 and 11 September 2002, respectively. Stations in the Fuji Network System affiliate Tōkai Television Broadcasting network started airing the series in the late night but moved it to late afternoons after the same series break. RahXephon thus remained both a late night and late afternoon anime series throughout its original run.