Downhole arrays provide enhanced understanding of dynamic soil behavior and site response. Historically, downhole array recordings have been available only for earthquakes with relatively limited durations. New recordings from a number of KiK-net downhole arrays during the 11 March 2011, M-w 9.0, subduction zone earthquake near the east coast of Honshu, Japan, allow us to investigate dynamic soil characteristics and site response due to long-duration subduction zone earthquakes. Using these recordings, we perform one-dimensional site response analyses to evaluate the applicability of commonly used analysis approaches under long-duration earthquakes. We find that site response analyses capture key features of measured surface response spectra particularly at soft rock/stiff soil sites subject to long-duration motion. However, at softer soil sites, it appears that the modulus reduction is overestimated and site-specific characterization is needed.