A liquid ejection apparatus includes an ejection port ejecting a liquid, a pressure chamber storing the liquid, an element generating energy for ejecting the liquid in the pressure chamber, first and second tanks which can store the liquid, a flow passage establishing communication between the first and second tanks through the pressure chamber, a switching unit switching a flowing direction of the liquid in the flow passage between a first direction from the first tank to the second tank and a second direction being opposite to the first direction, and a pressure compensation unit. When a pressure in a downstream side flow passage portion downstream of the pressure chamber has a predetermined pressure or below, the pressure compensation unit compensates for reduction in pressure in the downstream side flow passage portion by supplying the liquid to the downstream side flow passage portion.