According to one embodiment, an etching apparatus includes a stage in an etching chamber, the stage which holds one of a first substrate and a second substrate, a plasma generator in the etching chamber, the plasma generator which is opposite to the stage and irradiates an ion beam toward the stage, a grid which is provided between the plasma generator and the stage, a supporter supporting the stage, the supporter having a rotational axis in a direction in which the ion beam is irradiated, a controller which is configured to mount the first substrate on the stage and irradiate the ion beam with the beam angle larger than 0° to the first substrate, when an elapsed time from an end of an etching of a predetermined layer in the second substrate is equal to or larger than a predetermined time.