The removal of methanol with permselective membranes can improve the conversion of the transesterification reaction with methanol as the byproduct by shifting the equilibrium. However, the required membrane performance and favorable reaction conditions (e.g., catalyst weight, temperature, and the molar ratio of the reaction substrate) are not fully understood yet regarding membrane-assisted transesterification. We investigated the effect of methanol removal by the FAU-type zeolite membrane in the transesterification of methyl hexanoate and 1-hexanol theoretically and experimentally. First, we propose a kinetic model considering the catalytic reaction rate and methanol removal rate by the membrane. The reaction rate, equilibrium, and permeation rate constants were individually determined at 333–373 K by the catalytic reactions and vapor permeation experiments. The FAU-type zeolite membrane showed sufficiently high methanol separation performance for the reaction solutions. Moreover, the highest conversion was achieved 96% at the initial molar ratio of 1-hexanol/methyl hexanoate of 3 and 373 K. The improvement in the conversion could be explained by the equilibrium shift with the selective removal of methanol via the membrane. These suggest that our kinetic model is valid for the estimation of conversion increment for membrane-assisted transesterification.