Low-Ca boninites (LCB) are arc-related magmatic rocks enriched in large ion lithophile elements (LILE), light rare earth elements (LREE), Zr and Hf relative to medium to heavy REE (MREE-HREE). These signatures are commonly attributed to a unique slab-derived agent that metasomatized a depleted mantle source but their origin in such an agent remains enigmatic. We report andesite-hosted refractory spinel harzburgite xenoliths from the Kamchatka arc, which contain a series of orthopyroxene-rich veins; these veins range in thickness, the contents of clinopyroxene and amphibole and degrees of reaction with the host. Vein minerals in reaction zones with host harzburgites show progressive depletion in MREE-HREE at constant Zr-Hf and develop patterns (U-shaped REE with Zr-Hf spikes) that mimic those of LCB. Major and trace element modeling suggests that these veins (1) formed from a high-temperature (≥1400°C), MgO-rich (∼30 wt.%) and silicic (∼54 wt.% SiO2) initial melt, strongly depleted in Al2O3, TiO2and alkalis and (2) record fractionation of the initial melt to form hydrous liquids; the initial melt was equilibrated with metasomatized Kamchatka harzburgites and was similar in trace element abundances to island arc tholeiite (LREE-depleted to flat LREE-MREE patterns, low Nb and Ta but no significant Zr-Hf anomalies, high LILE). We argue that primary magmas of LCB formed by fluid-fluxed (LILE-rich and [Nb, Ta]-depleted fluid) melting of a cpx-free, highly refractory (≥30% melt extraction) harzburgitic source similar to arc peridotites from Kamchatka and elsewhere. This peculiar source may explain the distinctive major element features of LCB primary magmas. We propose that the primary magmas of LCB develop their characteristic trace element patterns through fractionation and reaction with refractory peridotites in the mantle wedge. Slab-related components alone may explain the high LILE in LCB but not their distinctive REE patterns and positive Zr-Hf anomalies.