The need to identify secondary sources of REEs and their recovery has led to the search for new methods and materials. In this study, a novel type of ion-imprinted adsorption membranes based on modified chitosan was synthesized. Their application for the recovery of chosen REEs from synthetic coal fly ash extracts was analyzed. The examined membranes were analyzed in terms of adsorption kinetics, isotherms, selectivity, reuse, and their separation abilities. The experimental data obtained were analyzed with two applications, namely, REE 2.0 and REE_isotherm. It was found that the adsorption of Nd3+ and Y3+ ions in the obtained membranes took place according to the chemisorption mechanism and was significantly controlled by film diffusion. The binding sites on the adsorbent surface were uniformly distributed; the examined ions showed the features of regular monolayer adsorption; and the adsorbents showed a strong affinity to the REE ions. The high values of Kd (900–1472.8 mL/g) demonstrate their high efficiency in the recovery of REEs. After five subsequent adsorption–desorption processes, approximately 85% of the value of one cycle was reached. The synthesized membranes showed a high rejection of the matrix components (Na, Mg, Ca, Al, Fe, and Si) in the extracts of the coal fly ashes, and the retention ratio for these Nd and Y ions was 90.11% and 80.95%, respectively.