Boron neutron capture therapy (BNCT) has recently attracted attention as a new cancer treatment option. In BNCT, boron compounds need to accumulate efficiently in tumor tissues to achieve excellent therapeutic effects. Therefore, it is highly desirable to develop a technology that can selectively and efficiently deliver boron compounds to tumors. In this study, we developed a novel fluorophenyl boronic acid (FPBA)-modified polyrotaxane (FPBA-PRX) and evaluated its potential as a tumor-selective boron compound for BNCT. FPBA-PRX is taken up by tumor cells through the binding between the FPBA moiety of FPBA-PRX and sialic acid on tumor cells. Importantly, the cellular uptake of FPBA-PRX was markedly higher than that of FPBA-modified cellulose (FPBA-CEL) because the FPBA moiety in FPBA-PRX was movable along with the axial chain of PRX, thereby avoiding a spatial mismatch between FPBA and sialic acid in tumor cells. Moreover, the accumulation of FPBA-PRX in the tumors after intravenous administration in mice was higher than that of FPBA-CEL. Furthermore, in vivo antitumor activity of FPBA-PRX was stronger than that of FPBA alone or commercially available boron compounds. These findings indicate the potential of FPBA-PRX as a tumor-selective boron compound for BNCT.