A vehicle body rear portion structure which can improve the operability of a coupling operation between a flange which extends downward from a peripheral portion of a parcel shelf and an upper end portion of a battery cover is provided. A battery 1 is mounted on a rear side of a seatback, a battery cover 5 which covers at least a rear surface of the battery 1 is provided, a parcel shelf 6 which extends to a vehicle rear side Rr from an upper end portion side of the seatback to cover an upper side of the above battery 1 is provided, a flange 16 which extends downward from a peripheral portion of the parcel shelf 6 and an upper end portion of the above battery cover 5 are coupled together by a coupling member, a retainer is mounted on the flange 16 of the parcel shelf 6 at an interval from a flange surface of the flange 16, and the flange 16, the upper end portion of the battery cover 5, and the retainer are coupled together by the coupling member 23 while the upper end portion of the battery cover is inserted between the flange 16 and the retainer.