To provide a method, etc., for cleaning a separation membrane which are capable of sufficiently removing not only the materials sticking and depositing on the membrane but even the materials infiltrated and left in the membrane by adsorption and settlement in cleaning the separation membrane.

The separation membrane 2 used for membrane separation of fluid to be treated is subjected to circulation cleaning of the membrane surface by feeding a liquid chemical Y for cleaning containing a surfactant to a region Sa on the non-permeation side of the separation membrane 2 (step S1), following which the separation membrane 2 is subjected to permeation cleaning of the separation membrane 2 by feeding a lower alcohol M to a region Sb on the permeation side with respect to the separation membrane 2 (step S2). Further, while the lower alcohol M is replaced with water W after the permeation cleaning, the further cleaning of the separation membrane 2 is executed (step S3).