A method for producing a rubber composition includes kneading: a rubber component comprising a conjugated diene polymer having at least one functional group selected from the group consisting of a thiol group, an oxetane group and a hydrocarbylthio group; silica particles; and a catalyst for condensing silanol to form an aggregate of the silica particles. Preferably, at least one polymer selected from the group consisting of a conjugate diene polymer having no functional group bondable to silica, and a polymer having no functional group bondable to silica and the polymer being other than conjugated diene polymer is also kneaded as a rubber component other than the conjugated diene polymer.