In bone tissue engineering, the intrinsic hydrophobicity and surface smoothness of three-dimensional (3D)-printed poly(ε-caprolactone) scaffolds hamper cell attachment, proliferation and differentiation. This intrinsic hydrophobicity of poly(ε-caprolactone) can be overcome by surface modifications, such as surface chemical modification or immobilization of biologically active molecules on the surface. Moreover, surface chemical modification may alter surface smoothness. Whether surface chemical modification or immobilization of a biologically active molecule on the surface is more effective to enhance pre-osteoblast proliferation and differentiation is currently unknown. Therefore, we aimed to investigate the osteogenic response of MC3T3-E1 pre-osteoblasts to chemically surface-modified and RGD-immobilized 3D-printed poly(ε-caprolactone) scaffolds. Poly(ε-caprolactone) scaffolds were 3D-printed consisting of strands deposited layer by layer with alternating 0°/90° lay-down pattern. 3D-printed poly(ε-caprolactone) scaffolds were surface-modified by either chemical modification using 3 M sodium hydroxide (NaOH) for 24 or 72 h, or by RGD-immobilization. Strands were visualized by scanning electron microscopy. MC3T3-E1 pre-osteoblasts were seeded onto the scaffolds and cultured up to 14 d. The strands of the unmodified poly(ε-caprolactone) scaffold had a smooth surface. NaOH treatment changed the scaffold surface topography from smooth to a honeycomb-like surface pattern, while RGD immobilization did not alter the surface topography. MC3T3-E1 pre-osteoblast seeding efficiency was similar (44%-54%) on all scaffolds after 12 h. Cell proliferation increased from day 1 to day 14 in unmodified controls (1.9-fold), 24 h NaOH-treated scaffolds (3-fold), 72 h NaOH-treated scaffolds (2.2-fold), and RGD-immobilized scaffolds (4.5-fold). At day 14, increased collagenous matrix deposition was achieved only on 24 h NaOH-treated (1.8-fold) and RGD-immobilized (2.2-fold) scaffolds compared to unmodified controls. Moreover, 24 h, but not 72 h, NaOH-treated scaffolds, increased alkaline phosphatase activity by 5-fold, while the increase by RGD immobilization was only 2.5-fold. Only 24 h NaOH-treated scaffolds enhanced mineralization (2.0-fold) compared to unmodified controls. In conclusion, RGD immobilization (0.011 μg mg-1 scaffold) on the surface and 24 h NaOH treatment of the surface of 3D-printed PCL scaffold both enhance pre-osteoblast proliferation and matrix deposition while only 24 h NaOH treatment results in increased osteogenic activity, making it the treatment of choice to promote bone formation by osteogenic cells.