This article presents the first operation of the magnetic circular dichroism (MCD) measurement system with periodic photon-helicity switching. The measurements were performed at the newly constructed soft x-ray beamline—BL23SU— at the third-generation synchrotron radiation facility, SPring-8. The monochromator control system was synchronized to the movement of the magnetic row (phase shift) of an APPLE-2 (Sasaki) type variably polarizing undulator. The periodic phase shift of the undulator provided the switching of helicity polarizing soft x rays up to 0.1 Hz. The closed-orbit distortion of the storage ring was controlled to avoid optical axis disturbances at this beamline as well as at other beamlines. The circular dichroism spectra with helicity switching by APPLE-2 show the possibility of high-sensitivity MCD measurements. This method promotes precise MCD measurements and can be a powerful technique to study magnetism as well as dichroism.