Literary sources attest that the gymnasium of the Athenian Academy was used from the 6th century BC to at least the 2nd century AD. The site, located based on texts and a horos stone, has been variously explored since 1929. Of the excavated structures, a rectangular courtyard building in the South has commonly been identified as the palaestra of the Academy gymnasium, whereas a large square peristyle building (so-called Tetragonos Peristylos) in the North has received little attention. This paper critically revises the identification of these two buildings and argues that the southern building, whose courtyard belongs to the Late Antique period, cannot have functioned as a palaestra. Instead, the square peristyle building, which was surrounded by rooms and dates to the 4th century BC, should be identified as a palaestra, due the plan and epigraphic evidence.