This paper investigates the effects on the blood compatibility of surface nanostructuring of Parylene-C coating. The proposed technique, based on the consecutive use of O2 and SF6 plasma, alters the surface roughness and enhances the intrinsic hydrophobicity of Parylene-C. The degree of hydrophobicity of the prepared surface can be precisely controlled by opportunely adjusting the plasma exposure times. Static contact angle measurements, performed on treated Parylene-C, showed a maximum contact angle of 158°. The nanostructured Parylene-C retained its hydrophobicity up to 45 days, when stored in a dry environment. Storing the samples in a body-mimicking solution caused the contact angle to progressively decrease. However, at the end of the measurement, the plasma treated surfaces still exhibited a higher hydrophobicity than the untreated counterparts. The proposed treatment improved the performance of the polymer as a water diffusion barrier in a body simulating environment. Modifying the nanotopography of the polymer influences the adsorption of different blood plasma proteins. The adsorption of albumin—a platelet adhesion inhibitor—and of fibrinogen—a platelet adhesion promoter—was studied by fluorescence microscopy. The adsorption capacity increased monotonically with increasing hydrophobicity for both studied proteins. The effect on albumin adsorption was considerably higher than on fibrinogen. Study of the proteins simultaneous adsorption showed that the albumin to fibrinogen adsorbed ratio increases with substrate hydrophobicity, suggesting lower thrombogenicity of the nanostructured surfaces. Animal experiments proved that the treated surfaces did not trigger any blood clot or thrombus formation when directly exposed to the arterial blood flow. The findings above, together with the exceptional mechanical and insulation properties of Parylene-C, support its use for packaging implants chronically exposed to the blood flow.