A novel branched side-chain-type sulfonated polyimide (6F-s-bSPI) membrane with accessible branching agents of melamine, hydrophobic trifluoromethyl groups (CF3), and flexible sulfoalkyl pendants is prepared by a high-temperature polycondensation and post-sulfonation method for use in vanadium redox flow batteries (VRFBs). The chemical structure of the 6F-s-bSPI membrane is confirmed by ATR-FTIR and 1H NMR spectra. The physico-chemical properties of the as-prepared 6F-s-bSPI membrane are systematically investigated and found to be strongly related to the specially designed structure. The 6F-s-bSPI membrane offers a reduced cost and possesses a significantly lowered vanadium ion permeability (1.18 × 10−7 cm2 min−1) compared to the linear SPI (2.25 × 10−7 cm2 min−1) and commercial Nafion 115 (1.36 × 10−6 cm2 min−1) membranes, prolonging the self-discharge duration of the VRFBs. In addition, the VRFB assembled with a 6F-s-bSPI membrane shows higher coulombic (98.3%–99.7%) and energy efficiencies (88.4%–66.12%) than that with a SPI or Nafion 115 membrane under current densities ranging from 20 to 100 mA cm−2. Moreover, the VRFB with a 6F-s-bSPI membrane delivers a stable cycling performance over 100 cycles with no decline in coulombic and energy efficiencies. These results show that the branched side-chain-type structure is a promising design to prepare excellent proton conductive membranes.