Disclosed is a bubble removing method in which fine bubbles are removed from a filter to improve the performance of the filter. The bubble removing method includes a step of degassing a processing liquid supplied from a supply source to prepare a highly degassed liquid (highly degassed liquid preparation), a step of supplying the prepared highly degassed liquid at a first processing liquid from a pump device to a filter device (temporary liquid permeation), a step of supplying the highly degassed liquid at a second processing liquid flow rate higher than the first processing liquid flow rate from the pump device to the filter device (initial liquid permeation), and a step of causing the highly degassed liquid to flow from the pump device to the filter device for a predetermined length of time (liquid permeation).