In this paper, the analysis of the responses of the pseudo dynamic test of two rectangular reinforced concrete (RC) bridge columns using the Hilbert-Huang transform (HHT) is introduced. Firstly, two 40%-scaled rectangular RC bridge columns are subjected to the pseudo dynamic test. The input of the pseudo dynamic test is set as the near-fault ground accelerations of the Chi-Chi Earthquake, which happened in 1999 in central Taiwan. After damage occurs to the bridge columns, we use non-shrinkage mortar to repair the columns, and then use 3 layers of CFRP to rehabilitate their plastic zone. The repaired bridge columns are again tested. Then we use the HHT to analyze the responses of the as-built and repaired bridge columns. The merit of applying the HHT to the responses of bridge columns is that it can transfer the displacement-time responses into instantaneous frequency responses, while the spectra are a function of both frequency and time. We can observe from the Hilbert spectra of the bridge columns that, at the instant when the frequency changes, the structural behavior changes from elastic to inelastic. The HHT can therefore be used to obtain the instantaneous natural frequencies of the bridge columns and to understand the relationship between the frequency changes and stiffness condition of the bridge columns.