Stereoscopic projection mapping (PM) allows a user to see a three-dimensional (3D) computer-generated (CG) object floating over physical surfaces of arbitrary shapes around us using projected imagery. However, the current stereoscopic PM technology only satisfies binocular cues and is not capable of providing correct focus cues, which causes a vergence--accommodation conflict (VAC). Therefore, we propose a multifocal approach to mitigate VAC in stereoscopic PM. Our primary technical contribution is to attach electrically focus-tunable lenses (ETLs) to active shutter glasses to control both vergence and accommodation. Specifically, we apply fast and periodical focal sweeps to the ETLs, which causes the "virtual image'" (as an optical term) of a scene observed through the ETLs to move back and forth during each sweep period. A 3D CG object is projected from a synchronized high-speed projector only when the virtual image of the projected imagery is located at a desired distance. This provides an observer with the correct focus cues required. In this study, we solve three technical issues that are unique to stereoscopic PM: (1) The 3D CG object is displayed on non-planar and even moving surfaces; (2) the physical surfaces need to be shown without the focus modulation; (3) the shutter glasses additionally need to be synchronized with the ETLs and the projector. We also develop a novel compensation technique to deal with the "lens breathing" artifact that varies the retinal size of the virtual image through focal length modulation. Further, using a proof-of-concept prototype, we demonstrate that our technique can present the virtual image of a target 3D CG object at the correct depth. Finally, we validate the advantage provided by our technique by comparing it with conventional stereoscopic PM using a user study on a depth-matching task.