This paper presents a numerical and experimental investigation regarding changes in dynamic characteristics (natural frequencies, mode shapes, and damping ratios) of encased steel profile of concrete-encased composite column-steel beam connections prior to and following lateral cyclic loading tests. To do so, four specimens with different column-beam connection details were considered. Pre-ambient vibration measurements were first conducted to extract experimental dynamic characteristics of encased steel profile in column-beam connections using enhanced frequency domain decomposition (EFDD) method in frequency domain and stochastic subspace identification (SSI) method in time-domain. Next, encased steel columns were enforced with longitudinal rebar, stirrups, and concrete to turn them into concrete-encased composite column. Lateral cyclic loading tests were performed on composite column-beam connections until failure. Concrete, stirrups, and rebar were removed and cleaned from the encased steel column after the cyclic loading tests. Post-ambient vibration measurements were repeated on the damaged models for further evaluation and comparisons. Additionally, 3D finite-element models of the samples were constituted using Abaqus program, and modal analyses were performed for each specimen to obtain the numerical dynamic characteristics and compare them with experimental results. The results show that natural frequencies distinctly decrease due to damages in the column-beam connection zones. The maximum decreases were calculated as 8.53% and 16.01% in EPCSB-I; 6.92% and 16.44% in EPCSB-II; 17.38% and 12.20% in EPCSB-III; as well as 23.10% and 22.85% in EPCSB-IV for EFDD and SSI methods, respectively. Also, after the cyclic loading tests, increasing of flexibility and rotational movements due to the decrease in joint stiffness has affected the mode shapes. When the initial finite-element analyses and experimental results were compared with each other, the maximum differences were obtained between 0.18% and 8.99% for EPCSB-I, 2.62% and 25.27% for EPCSB-II, 0.84% and 28.60% for EPCSB-III, and 0.19% and 29.87% for EPCSB-IV, respectively.