MoSe2, with high theoretical specific capacity, has attracted a lot of attention. There remains an open challenge to effectively suppress the irreversible selenium dissolution and rapid capacity decrease induced by severe volume change during cycling. Herein, we synthesize MoSe2 nanoflowers dispersed on one-dimensional (1D) N-doped carbon nanofibers (MoSe2@NCNFs) for use as a freestanding electrode. In this unique structure, the 1D N-doped carbon nanofibers are found to not only enhance the conductivity but also ensure the structural integrity during the Li+/Na+ insertion/destraction processes. As expected, at 2 A·g−1, the specific capacity of the MoSe2@NCNFs is maintained at 180 mAh·g−1 after 500 cycles when used in lithium storage applications. Furthermore, in the case of sodium storage, at 1 A·g−1, the MoSe2@NCNFs shows a capacity of 122 mAh·g−1 after 500 cycles. These findings suggest that the MoSe2@NCNF electrodes may be a promising candidate for use in reversible Li/Na storage applications.