A semiconductor memory device includes a controller programming a nonvolatile memory cell by applying a first pulse so that a charge amount smaller than a target charge amount is accumulated in the nonvolatile memory cell, a second pulse train so that a second charge amount smaller than the target charge amount and larger than the first charge amount is accumulated in the nonvolatile memory cell, and a third pulse train so that a third charge amount falling within an allowable error range of the target charge amount is accumulated. The semiconductor memory cell includes a gate electrode formed on a semiconductor layer via a gate insulating film, a channel region disposed under the gate electrode, diffusion regions disposed on both sides of the channel region and memory functional units formed on both sides of the gate electrode.