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, Mw 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.