A method of fabricating a color filter is provided. First, a substrate having a light shielding layer formed thereon is provided, wherein the light shielding layer is adopted for defining a plurality of sub-pixel regions on the substrate. Next, a hydrophobic layer is formed on the light shielding layer by stencil printing, or a surface silylation treatment is carried out to clean the light shielding layer by inkjet printing. Next, a color filter layer is formed in the sub-pixel regions. Thus, fabrication method of the present invention is capable of reducing the possibility of intermixing the color ink between adjacent sub-pixel regions.