Application of low-magnitude strains to cells on small-thickness scaffolds, such as those for rodent calvarial defect models, is problematic, because general translation systems have limitations in terms of generating low-magnitude smooth signals. To overcome this limitation, we developed a cyclic strain generator using a customized, flexure-based, translational nanoactuator that enabled generation of low-magnitude smooth strains at the subnano- to micrometer scale to cells on small-thickness scaffolds. The cyclic strain generator we developed showed predictable operational characteristics by generating a sinusoidal signal of a few micrometers (4.5 μm) without any distortion. Three-dimensional scaffolds fitting the critical-size rat calvarial defect model were fabricated using poly(caprolactone), poly(lactic-co-glycolic acid), and tricalcium phosphate. Stimulation of human adipose-derived stem cells (ASCs) on these fabricated scaffolds using the cyclic strain generator we developed resulted in upregulated osteogenic marker expression compared to the nonstimulated group. These preliminary in vitro results suggest that the cyclic strain generator successfully provided mechanical stimulation to cells on small-thickness scaffolds, which influenced the osteogenic differentiation of ASCs.