The extent of partial melting of peridotites is a function of temperature, pressure, and fluid supply. Understanding the petrogenesis of ultra-depleted peridotites is important for elucidating mantle potential temperature and the role of water in the mantle. We analyzed the major and trace element compositions of ultra-depleted peridotites from the Kamuikotan zone, Japan. Geochemical models were then generated to constrain the melting conditions and their relation to boninitic melts. The peridotites are characterized by minerals with high Mg/Fe and Cr/Al ratios, and olivine and orthopyroxene with low Ti and Y contents. The mineral compositions suggest that these peridotites are among the most depleted peridotites on Earth. Orthopyroxene compositions characterized by Zr and Sr enrichments relative to Ti and Y depletion cannot be solely explained by melt extraction from typical mantle compositions. Modeling of influx melting reproduces orthopyroxene trace element compositions of ultra-depleted harzburgites formed after high degrees (>30%) of slab-fluid influx melting at a low influx rate and melt fraction. The instantaneous fractional melts equilibrated with residues produced by the melting model and the melts, which equilibrated with amphiboles have similar trace elements patterns as boninites. However, the instantaneous fractional melts have low trace element abundances indicating that ultra-depleted harzburgites are residues after extraction of refractory melts. Boninites are probably accumulated melts formed during the melting processes, or fractionated melt from the instantaneous fractional melts. High temperatures (>1350°C) and continuous fluid supply are key to the formation of ultra-depleted peridotites and boninites during subduction initiation.