A frequency error estimation is presented for the isogeometric free vibration analysis of Kirchhoff–Love cylindrical shells using both quadratic and cubic basis functions. By analyzing the discrete isogeometric equations with the aid of harmonic wave assumption, the frequency error measures are rationally derived for the quadratic and cubic formulations for Kirchhoff–Love cylindrical shells. In particular, the governing relationship of the continuum frequency for Kirchhoff–Love cylindrical shells is naturally embedded into the frequency error measures without the need of explicit frequency expressions, which usually are not trivial for the shell problems. In accordance with these theoretical findings, the 2nd and 4th orders of frequency accuracy are attained for the isogeometric schemes using quadratic and cubic basis functions, respectively. Numerical results not only thoroughly verify the theoretical convergence rates of frequency solutions, but also manifest an excellent magnitude match between numerical and theoretical frequency errors for the isogeometric free vibration analysis of Kirchhoff–Love cylindrical shells.