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We investigated how end-functionalized solution styrene–butadiene rubber (SSBR) affects the vulcanizate structures and the physical properties of silica-filled vulcanizates using non-functionalized and end-functionalized SSBRs with aminopropylalkoxysilane. Two silane agents were used. Triethoxy(octyl)silane was used as a covering agent, and bis-[3-(triethoxysilyl)propyl]disulfide was applied as a coupling agent. The effects of three different silica–silane systems with a covering agent (CV), a coupling agent (CP), or with no silane (NS) were analyzed. In the CV and NS systems, the cross-link densities induced by the polymer and curing system were similar with respect to the end-functionalization. Further, the cross-link densities induced by the silica–silane system were similar, regardless of the end-functionalization. However, the CP system exhibited similar cross-link densities, irrespective of functionalization. Both the coupling agent and end-functional group chemically bonded with the silanol groups of silica, thus competing with each other and affecting the vulcanizate structure. However, increasing the silica content decreased the effect of end-functionalization because the content of the coupling agent increased, and the end-functional group was less mobile than the coupling agent's alkoxy group.