This work updates the FE models for 25- and 42-story tall buildings having walls or a shear core as a major lateral force-resisting system, utilizing modal parameters such as natural frequencies, and mode shapes identified from measured vibration records in a previous study. Automated FE model updating adopting optimization theory includes a series of procedures that estimate sensitivity matrices, unknown parameters (based on a Bayesian technique), and correlation coefficients. A simplified FE model, considering 3 stiffnesses and 3 masses at each story as structural parameters, was derived from the analysis results of a more detailed 3D-FE model normally used in design practice, and was employed as the starting model for the update process. Although the test and analysis values of the natural frequency and mode shape for the lower three modes currently considered were in excellent agreement, many stories in both buildings exhibited a significant increase in stiffness, approximately 100%, and decrease in mass, approximately 50%. However, given that the natural frequencies from a 3D-FE analysis were found to be approximately 1.5 times as small as than the measured frequencies, at least for the three lower modes in both of them, this is unsurprising. Furthermore, the detailed 3D-FE model developed in the design office could be subject to a number of practical uncertainties/inaccuracies. This supports the conclusion is that the contemporary domestic design practice for FE analysis remains very conservative. It is shown that the proposed FE model updating technique using output-only modal data can be effectively applied to determine uncertain structural behavior or parameters and employed in the damage detection or structural health monitoring fields.