The Kashima Lighthouse, one of the lighthouses that suffered damage in the 2011 Great East Japan Earthquake, required a careful investigation to estimate its long-term behavior and seismic vulnerability. This study, therefore, undertook a meticulous process of the dynamic testing, dynamic identification, and long-term structural health monitoring of the Kashima Lighthouse. The results of dynamic tests reveal that the fundamental frequencies of the Kashima Lighthouse are estimated to be around 2.60 Hz and 2.63 Hz in the east–west and north–south directions, respectively. The natural modes and damping factors are identified using an SSIM (Stochastic Subspace Identification Method). This paper also discusses the result of long-term structural health monitoring, where machine learning techniques were applied for data processing, highlighting the rigor and thoroughness of this research.