A method of selectively separating a phospholipid from a sample solution containing the phospholipid is provided. The method comprises: adsorbing calcium ions to a filler, at least a surface of the filler being constituted of a calcium phosphate-based compound; supplying the sample solution into an apparatus having a filling space, wherein the filling space being filled with the filler so that the phospholipid contained in the sample solution is adsorbed to the filler through the calcium ions; supplying an organic solvent-based eluate into the filling space of the apparatus to obtain a liquid containing the phospholipid and discharged from the apparatus; and fractionating the obtained liquid per a predetermined amount to thereby separate the phospholipid from the sample solution.